#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_ACHILLES_Lineage_Results_Top_Genes	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ATG4B	23192	hgsc.bcm.edu	37	2	242610738	242610738	+	Silent	SNP	T	T	C	rs11538896	byFrequency	TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr2:242610738T>C	ENST00000404914.3	+	12	1129	c.1026T>C	c.(1024-1026)ctT>ctC	p.L342L	ATG4B_ENST00000474739.2_Silent_p.L328L|ATG4B_ENST00000402096.1_Silent_p.L268L|ATG4B_ENST00000405546.3_Silent_p.L342L|ATG4B_ENST00000396411.3_Silent_p.L268L	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	342					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		TGTCTCTGCTTGGAGGTGCCC	0.627													C|||	1027	0.205072	0.0787	0.2089	5008	,	,		19333	0.2966		0.2336	False		,,,				2504	0.2495				Melanoma(78;458 1323 6342 12171 39523)												0								C	,	413,3859		23,367,1746	65.0	71.0	69.0		1026,1026	-9.1	0.0	2	dbSNP_120	69	1876,6578		229,1418,2580	no	coding-synonymous,coding-synonymous	ATG4B	NM_013325.4,NM_178326.2	,	252,1785,4326	CC,CT,TT		22.1907,9.6676,17.9868	,	342/394,342/381	242610738	2289,10437	2136	4227	6363	SO:0001819	synonymous_variant	23192			AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"""APG4 autophagy 4 homolog B (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog B (S. cerevisiae)"""	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.1026T>C	2.37:g.242610738T>C		Somatic		WXS	SOLID	Phase_I	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Silent	SNP	ENST00000404914.3	37	CCDS46564.1																																																																																				0.627	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3		NM_013325	
BMP3	651	hgsc.bcm.edu	37	4	81967319	81967319	+	Silent	SNP	C	C	T			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr4:81967319C>T	ENST00000282701.2	+	2	1064	c.744C>T	c.(742-744)gcC>gcT	p.A248A		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	248					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)	p.A248A(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						ATGATGCCGCCATTTCTGAGC	0.478																																																	1	Substitution - coding silent(1)	central_nervous_system(1)											97.0	98.0	98.0					4																	81967319		2203	4300	6503	SO:0001819	synonymous_variant	651			M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.744C>T	4.37:g.81967319C>T		Somatic		WXS	SOLID	Phase_I	Q4VAS5	Silent	SNP	ENST00000282701.2	37	CCDS3588.1																																																																																				0.478	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			
C1orf101	257044	hgsc.bcm.edu;ucsc.edu	37	1	244780931	244780931	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr1:244780931C>T	ENST00000366534.4	+	20	2645	c.2591C>T	c.(2590-2592)cCc>cTc	p.P864L	C1orf101_ENST00000366533.4_Intron|C1orf101_ENST00000366531.3_Missense_Mutation_p.P713L	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	864						CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			ATATTTTGGCCCATGGGCCAT	0.348																																																	0													226.0	184.0	197.0					1																	244780931		692	1588	2280	SO:0001583	missense	257044			BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397			28491	protein-coding gene	gene with protein product						12477932	Standard	NM_173807		Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.2591C>T	1.37:g.244780931C>T	ENSP00000355492:p.Pro864Leu	Somatic		WXS	SOLID	Phase_I	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Missense_Mutation	SNP	ENST00000366534.4	37	CCDS44340.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070991	0.36566	.	.	ENSG00000179397	ENST00000366534;ENST00000428042;ENST00000366531	T;T;T	0.24908	1.83;1.83;1.83	5.73	4.74	0.60224	.	0.204155	0.34362	N	0.004036	T	0.46678	0.1405	L	0.58101	1.795	0.39915	D	0.974072	D;D	0.89917	1.0;0.993	D;P	0.77557	0.99;0.865	T	0.45234	-0.9275	10	0.66056	D	0.02	.	14.6769	0.68986	0.1549:0.8451:0.0:0.0	.	784;864	B1AQM6;Q5SY80	.;CA101_HUMAN	L	864;784;713	ENSP00000355492:P864L;ENSP00000395796:P784L;ENSP00000355489:P713L	ENSP00000355489:P713L	P	+	2	0	C1orf101	242847554	0.814000	0.29104	0.964000	0.40570	0.076000	0.17211	1.460000	0.35244	2.716000	0.92895	0.655000	0.94253	CCC		0.348	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1		NM_173807	
CALML5	51806	hgsc.bcm.edu	37	10	5541230	5541230	+	Missense_Mutation	SNP	T	T	C	rs11546426	byFrequency	TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr10:5541230T>C	ENST00000380332.3	-	1	303	c.172A>G	c.(172-174)Agc>Ggc	p.S58G		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	58	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		S -> G (polymorphism confirmed at protein level; dbSNP:rs11546426). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105}.		epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						TCGCCGTCGCTGTCAACCTCG	0.652													T|||	1487	0.296925	0.4493	0.2133	5008	,	,		17834	0.2014		0.2972	False		,,,				2504	0.2485				GBM(149;1055 3356 43077)												0								T	GLY/SER	1804,2602	530.3+/-372.9	367,1070,766	73.0	74.0	74.0		172	0.6	0.0	10	dbSNP_120	74	2610,5990	422.1+/-353.9	433,1744,2123	yes	missense	CALML5	NM_017422.4	56	800,2814,2889	CC,CT,TT		30.3488,40.9442,33.9382	possibly-damaging	58/147	5541230	4414,8592	2203	4300	6503	SO:0001583	missense	51806			AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.172A>G	10.37:g.5541230T>C	ENSP00000369689:p.Ser58Gly	Somatic		WXS	SOLID	Phase_I	Q5SQI3|Q8IXU8	Missense_Mutation	SNP	ENST00000380332.3	37	CCDS7068.1	632	0.2893772893772894	218	0.44308943089430897	82	0.2265193370165746	112	0.1958041958041958	220	0.29023746701846964	T	14.35	2.509974	0.44660	0.409442	0.303488	ENSG00000178372	ENST00000380332	T	0.72505	-0.66	4.6	0.628	0.17681	EF-hand-like domain (1);	0.913192	0.09252	N	0.827796	T	0.00012	0.0000	L	0.31578	0.945	0.80722	P	0.0	B	0.13145	0.007	B	0.12837	0.008	T	0.32508	-0.9904	9	0.87932	D	0	-10.236	3.7075	0.08407	0.1584:0.2953:0.0:0.5463	rs11546426;rs17853880	58	Q9NZT1	CALL5_HUMAN	G	58	ENSP00000369689:S58G	ENSP00000369689:S58G	S	-	1	0	CALML5	5531230	0.649000	0.27322	0.001000	0.08648	0.000000	0.00434	0.567000	0.23608	-0.000000	0.14550	-0.408000	0.06270	AGC		0.652	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1		NM_017422	
CLMN	79789	hgsc.bcm.edu;ucsc.edu	37	14	95657993	95657993	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr14:95657993G>A	ENST00000298912.4	-	13	3030	c.2917C>T	c.(2917-2919)Cag>Tag	p.Q973*	CLMN_ENST00000557215.1_5'UTR|CLMN_ENST00000556441.1_Nonsense_Mutation_p.Q38*	NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	973					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		TCCGGCTGCTGGACAAGCTGT	0.527																																																	0													82.0	84.0	84.0					14																	95657993		2203	4300	6503	SO:0001587	stop_gained	79789			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2917C>T	14.37:g.95657993G>A	ENSP00000298912:p.Gln973*	Somatic		WXS	SOLID	Phase_I	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Nonsense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	G	36	5.632912	0.96682	.	.	ENSG00000165959	ENST00000298912;ENST00000556441	.	.	.	4.99	4.99	0.66335	.	0.000000	0.37761	N	0.001943	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	13.7968	0.63175	0.0:0.0:1.0:0.0	.	.	.	.	X	973;38	.	ENSP00000298912:Q973X	Q	-	1	0	CLMN	94727746	0.998000	0.40836	0.963000	0.40424	0.006000	0.05464	3.335000	0.52105	2.320000	0.78422	0.561000	0.74099	CAG		0.527	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			
COL5A1	1289	hgsc.bcm.edu	37	9	137660274	137660274	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr9:137660274G>A	ENST00000371817.3	+	25	2665	c.2251G>A	c.(2251-2253)Ggc>Agc	p.G751S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	751	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GGGGAAACCAGGCCTTCCAGG	0.617																																																	0													137.0	143.0	141.0					9																	137660274		2203	4300	6503	SO:0001583	missense	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2251G>A	9.37:g.137660274G>A	ENSP00000360882:p.Gly751Ser	Somatic		WXS	SOLID	Phase_I	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.486096	0.63962	.	.	ENSG00000130635	ENST00000371817	D	0.99329	-5.75	4.44	4.44	0.53790	.	0.000000	0.85682	U	0.000000	D	0.99563	0.9843	H	0.96430	3.82	0.49389	D	0.999789	D	0.89917	1.0	D	0.83275	0.996	D	0.97971	1.0343	10	0.87932	D	0	.	12.5593	0.56271	0.0:0.0:1.0:0.0	.	751	P20908	CO5A1_HUMAN	S	751	ENSP00000360882:G751S	ENSP00000360882:G751S	G	+	1	0	COL5A1	136800095	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.790000	0.62453	2.027000	0.59764	0.561000	0.74099	GGC		0.617	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2		NM_000093	
COL9A1	1297	hgsc.bcm.edu	37	6	70942325	70942325	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr6:70942325T>A	ENST00000357250.6	-	36	2622	c.2464A>T	c.(2464-2466)Aag>Tag	p.K822*	COL9A1_ENST00000370499.4_Nonsense_Mutation_p.K579*|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000320755.7_Nonsense_Mutation_p.K579*|RP1-149L1.1_ENST00000522264.1_RNA	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	822	Collagen-like 9.|Triple-helical region (COL1).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						GGGGGCCCCTTAATGCCCGGA	0.557																																																	0													96.0	104.0	101.0					6																	70942325		2203	4300	6503	SO:0001587	stop_gained	1297				CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.2464A>T	6.37:g.70942325T>A	ENSP00000349790:p.Lys822*	Somatic		WXS	SOLID	Phase_I	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Nonsense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	T	37	6.224266	0.97390	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	.	.	.	5.81	5.81	0.92471	.	0.042391	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.1699	0.81801	0.0:0.0:0.0:1.0	.	.	.	.	X	822;579;579	.	ENSP00000315252:K579X	K	-	1	0	COL9A1	70999046	1.000000	0.71417	0.991000	0.47740	0.446000	0.32137	7.936000	0.87665	2.217000	0.71921	0.533000	0.62120	AAG		0.557	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			
DSCAML1	57453	hgsc.bcm.edu	37	11	117387317	117387317	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr11:117387317G>T	ENST00000321322.6	-	8	1829	c.1828C>A	c.(1828-1830)Cgc>Agc	p.R610S	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R340S	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	550	Ig-like C2-type 7.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		ACCACCTGGCGGTGGTTGTCT	0.587																																																	0													95.0	76.0	82.0					11																	117387317		2201	4296	6497	SO:0001583	missense	57453				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1828C>A	11.37:g.117387317G>T	ENSP00000315465:p.Arg610Ser	Somatic		WXS	SOLID	Phase_I	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	17.85	3.491204	0.64074	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.66460	-0.21;-0.21	4.1	3.15	0.36227	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82554	0.5062	M	0.90814	3.15	0.58432	D	0.999999	D	0.71674	0.998	D	0.71184	0.972	D	0.85108	0.0961	9	0.87932	D	0	.	11.2752	0.49163	0.0:0.0:0.6685:0.3315	.	550	Q8TD84	DSCL1_HUMAN	S	340;610;317	ENSP00000434335:R340S;ENSP00000315465:R610S	ENSP00000315465:R610S	R	-	1	0	DSCAML1	116892527	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.415000	0.59809	1.017000	0.39495	0.462000	0.41574	CGC		0.587	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2		NM_020693	
EDN3	1908	hgsc.bcm.edu	37	20	57896170	57896170	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr20:57896170C>G	ENST00000337938.2	+	3	850	c.464C>G	c.(463-465)cCa>cGa	p.P155R	EDN3_ENST00000371025.3_Missense_Mutation_p.P155R|EDN3_ENST00000311585.7_Missense_Mutation_p.P155R|EDN3_ENST00000395654.3_Missense_Mutation_p.P155R|EDN3_ENST00000371028.2_Missense_Mutation_p.P155R	NM_207034.1	NP_996917.1	P14138	EDN3_HUMAN	endothelin 3	155					blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|inositol phosphate-mediated signaling (GO:0048016)|melanocyte differentiation (GO:0030318)|multicellular organismal development (GO:0007275)|neural crest cell migration (GO:0001755)|neuron differentiation (GO:0030182)|neutrophil chemotaxis (GO:0030593)|peptide hormone secretion (GO:0030072)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|regulation of developmental pigmentation (GO:0048070)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|signal transduction (GO:0007165)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	19	all_lung(29;0.0115)					TCACATCGGCCACACTTGCGC	0.577																																																	0													115.0	105.0	109.0					20																	57896170		2203	4300	6503	SO:0001583	missense	1908			X52001	CCDS13477.1, CCDS13478.1, CCDS13479.1	20q13.2-q13.3	2013-02-26			ENSG00000124205	ENSG00000124205		"""Endogenous ligands"""	3178	protein-coding gene	gene with protein product		131242					Standard	NM_000114		Approved	ET3	uc002yaq.3	P14138	OTTHUMG00000032867	ENST00000337938.2:c.464C>G	20.37:g.57896170C>G	ENSP00000337128:p.Pro155Arg	Somatic		WXS	SOLID	Phase_I	E1P5I5|Q03229|Q7Z6D2|Q9UGT7	Missense_Mutation	SNP	ENST00000337938.2	37	CCDS13477.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.506521	0.26949	.	.	ENSG00000124205	ENST00000337938;ENST00000311585;ENST00000371028;ENST00000371025;ENST00000395654	D;D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36;-2.36	4.87	3.9	0.45041	.	0.641603	0.13820	N	0.360520	D	0.87269	0.6135	L	0.34521	1.04	0.09310	N	1	P;D;P;P	0.54964	0.914;0.969;0.86;0.93	P;P;B;B	0.51806	0.581;0.68;0.272;0.289	T	0.78344	-0.2240	10	0.54805	T	0.06	-1.7006	10.6787	0.45802	0.1912:0.8088:0.0:0.0	.	155;155;155;155	P14138-2;Q7Z6D2;P14138;Q4FAT2	.;.;EDN3_HUMAN;.	R	155	ENSP00000337128:P155R;ENSP00000311854:P155R;ENSP00000360067:P155R;ENSP00000360064:P155R;ENSP00000379015:P155R	ENSP00000311854:P155R	P	+	2	0	EDN3	57329565	0.163000	0.22920	0.002000	0.10522	0.001000	0.01503	1.324000	0.33712	1.132000	0.42129	0.561000	0.74099	CCA		0.577	EDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079919.2		NM_000114	
EGFL6	25975	hgsc.bcm.edu	37	X	13618146	13618146	+	Silent	SNP	T	T	C			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chrX:13618146T>C	ENST00000361306.1	+	4	590	c.333T>C	c.(331-333)aaT>aaC	p.N111N	EGFL6_ENST00000380602.3_Silent_p.N111N	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	111	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						GATGTGTGAATACACACGGAA	0.478																																																	0													146.0	108.0	121.0					X																	13618146		2203	4300	6503	SO:0001819	synonymous_variant	25975			AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.333T>C	X.37:g.13618146T>C		Somatic		WXS	SOLID	Phase_I	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	37	CCDS14155.1																																																																																				0.478	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1		NM_015507	
FOXN3	1112	hgsc.bcm.edu	37	14	89878773	89878773	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr14:89878773A>C	ENST00000345097.4	-	2	164	c.48T>G	c.(46-48)atT>atG	p.I16M	RP11-33N16.2_ENST00000556383.1_RNA|FOXN3_ENST00000557258.1_Missense_Mutation_p.I16M|FOXN3_ENST00000555353.1_Missense_Mutation_p.I16M|FOXN3_ENST00000261302.5_Missense_Mutation_p.I16M|RP11-33N16.3_ENST00000555070.1_RNA	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	16					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGGAGACACTAATTCCTGAGC	0.512																																																	0													58.0	59.0	58.0					14																	89878773		2203	4300	6503	SO:0001583	missense	1112				CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254		"""Forkhead boxes"""	1928	protein-coding gene	gene with protein product		602628	"""chromosome 14 open reading frame 116"", ""checkpoint suppressor 1"""	C14orf116, CHES1		9154802	Standard	NM_005197		Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.48T>G	14.37:g.89878773A>C	ENSP00000343288:p.Ile16Met	Somatic		WXS	SOLID	Phase_I	Q96II7|Q9UIE7	Missense_Mutation	SNP	ENST00000345097.4	37	CCDS41977.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.712591	0.48517	.	.	ENSG00000053254	ENST00000345097;ENST00000261302;ENST00000557258;ENST00000555353;ENST00000555855;ENST00000555034;ENST00000553904	T;T;T;T;D	0.95342	-0.04;-0.04;-0.04;-0.04;-3.68	5.54	-1.74	0.08056	.	0.133168	0.52532	D	0.000078	D	0.91838	0.7417	L	0.54323	1.7	0.32941	D	0.518457	P;P	0.51351	0.944;0.773	B;P	0.48840	0.388;0.592	D	0.89327	0.3644	10	0.42905	T	0.14	.	7.6656	0.28428	0.297:0.0:0.4927:0.2103	.	16;16	O00409;O00409-2	FOXN3_HUMAN;.	M	16	ENSP00000343288:I16M;ENSP00000261302:I16M;ENSP00000452005:I16M;ENSP00000452227:I16M;ENSP00000451135:I16M	ENSP00000261302:I16M	I	-	3	3	FOXN3	88948526	0.992000	0.36948	0.942000	0.38095	0.959000	0.62525	0.527000	0.22987	-0.567000	0.06046	-0.408000	0.06270	ATT		0.512	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410902.2		NM_005197	
HHIP	64399	hgsc.bcm.edu	37	4	145580833	145580833	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr4:145580833G>T	ENST00000296575.3	+	4	1329	c.674G>T	c.(673-675)gGg>gTg	p.G225V	HHIP_ENST00000511314.1_3'UTR|HHIP_ENST00000434550.2_Missense_Mutation_p.G225V|HHIP-AS1_ENST00000512359.1_RNA	NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	225					carbohydrate metabolic process (GO:0005975)|dorsal/ventral pattern formation (GO:0009953)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|negative regulation of signal transduction (GO:0009968)|negative regulation of smoothened signaling pathway (GO:0045879)|neuroblast proliferation (GO:0007405)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|skeletal system morphogenesis (GO:0048705)|smoothened signaling pathway (GO:0007224)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	hedgehog family protein binding (GO:0097108)|oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0185)		GTTGTGAGTGGGCTGCGGCAG	0.458																																																	0													125.0	138.0	133.0					4																	145580833		2203	4300	6503	SO:0001583	missense	64399			AK024645	CCDS3762.1	4q31.21-q31.3	2008-08-29	2001-11-29		ENSG00000164161	ENSG00000164161			14866	protein-coding gene	gene with protein product		606178	"""hedgehog-interacting protein"""			11435703, 11731473	Standard	NM_022475		Approved	HIP, FLJ20992	uc003ijs.2	Q96QV1	OTTHUMG00000161428	ENST00000296575.3:c.674G>T	4.37:g.145580833G>T	ENSP00000296575:p.Gly225Val	Somatic		WXS	SOLID	Phase_I	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Missense_Mutation	SNP	ENST00000296575.3	37	CCDS3762.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.833106	0.91036	.	.	ENSG00000164161	ENST00000296575;ENST00000434550	T;T	0.54675	2.44;0.56	5.54	5.54	0.83059	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.77280	0.4107	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.80591	-0.1314	10	0.87932	D	0	-15.0322	19.4725	0.94969	0.0:0.0:1.0:0.0	.	225;225	Q96QV1;Q96QV1-2	HHIP_HUMAN;.	V	225	ENSP00000296575:G225V;ENSP00000408587:G225V	ENSP00000296575:G225V	G	+	2	0	HHIP	145800283	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.869000	0.99810	2.620000	0.88729	0.555000	0.69702	GGG		0.458	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			
ISY1	57461	hgsc.bcm.edu;ucsc.edu	37	3	128864701	128864701	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr3:128864701A>T	ENST00000393295.3	-	6	520	c.203T>A	c.(202-204)tTt>tAt	p.F68Y	ISY1-RAB43_ENST00000418265.1_Missense_Mutation_p.F68Y|ISY1_ENST00000393292.3_Missense_Mutation_p.F68Y|ISY1_ENST00000273541.8_Missense_Mutation_p.F68Y|ISY1_ENST00000471497.1_5'UTR	NM_001199469.1|NM_020701.3	NP_001186398.1|NP_065752.1	Q9ULR0	ISY1_HUMAN	ISY1 splicing factor homolog (S. cerevisiae)	68					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|skin(1)	15						ACGAATTCGAAATTCACCTAA	0.393																																																	0													87.0	84.0	85.0					3																	128864701		1886	4115	6001	SO:0001583	missense	57461				CCDS43149.1, CCDS56277.1	3q21.3	2008-11-25			ENSG00000240682	ENSG00000240682			29201	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 33"""	612764				16103217	Standard	NM_020701		Approved	KIAA1160, fSAP33		Q9ULR0	OTTHUMG00000137365	ENST00000393295.3:c.203T>A	3.37:g.128864701A>T	ENSP00000376973:p.Phe68Tyr	Somatic		WXS	SOLID	Phase_I	Q96IL2|Q9BT05	Missense_Mutation	SNP	ENST00000393295.3	37	CCDS43149.1	.	.	.	.	.	.	.	.	.	.	A	14.66	2.602310	0.46423	.	.	ENSG00000240682	ENST00000418265;ENST00000393295;ENST00000273541;ENST00000496163;ENST00000393292	T	0.28895	1.59	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	L	0.33293	1	0.80722	D	1	B;B;B	0.29671	0.073;0.254;0.065	B;B;B	0.38106	0.042;0.265;0.06	T	0.02893	-1.1097	10	0.05721	T	0.95	.	13.2342	0.59961	1.0:0.0:0.0:0.0	.	68;68;68	Q9ULR0-2;Q9ULR0;Q9ULR0-1	.;ISY1_HUMAN;.	Y	68;68;68;6;68	ENSP00000273541:F68Y	ENSP00000273541:F68Y	F	-	2	0	ISY1	130347391	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.662000	0.91130	2.010000	0.58986	0.482000	0.46254	TTT		0.393	ISY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267856.1		NM_020701	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651228	1651228	+	Missense_Mutation	SNP	C	C	G	rs71454096	byFrequency	TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr11:1651228C>G	ENST00000399676.2	+	1	196	c.158C>G	c.(157-159)gCg>gGg	p.A53G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	53				A -> G (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		tccggctgtgcgggctgtggg	0.682													g|||	3279	0.654752	0.7784	0.6225	5008	,	,		5668	0.4157		0.7406	False		,,,				2504	0.6687																0								G	GLY/ALA	3099,1107		1207,685,211	30.0	39.0	36.0		158	2.2	0.4	11	dbSNP_130	36	5885,2399		2219,1447,476	no	missense	KRTAP5-5	NM_001001480.2	60	3426,2132,687	GG,GC,CC		28.9594,26.3195,28.0705	benign	53/238	1651228	8984,3506	2103	4142	6245	SO:0001583	missense	439915			AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.158C>G	11.37:g.1651228C>G	ENSP00000382584:p.Ala53Gly	Somatic		WXS	SOLID	Phase_I	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	1420	0.6501831501831502	378	0.7682926829268293	245	0.6767955801104972	240	0.4195804195804196	557	0.7348284960422163	N	3.130	-0.178731	0.06380	0.736805	0.710406	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01084	5.36	2.19	2.19	0.27852	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02925	-1.1093	8	0.46703	T	0.11	.	7.2847	0.26330	0.0:0.2785:0.7215:0.0	.	53	Q701N2	KRA55_HUMAN	G	53;51	ENSP00000382584:A53G	ENSP00000382584:A53G	A	+	2	0	KRTAP5-5	1607804	0.123000	0.22298	0.392000	0.26245	0.247000	0.25773	0.000000	0.12993	0.229000	0.21039	-0.415000	0.06103	GCG		0.682	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			
MARCH2	51257	hgsc.bcm.edu	37	19	8486884	8486884	+	Missense_Mutation	SNP	G	G	A	rs1133893	byFrequency	TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr19:8486884G>A	ENST00000602117.1	+	2	615	c.160G>A	c.(160-162)Gcc>Acc	p.A54T	MARCH2_ENST00000381035.4_Missense_Mutation_p.A54T|MARCH2_ENST00000393944.1_Missense_Mutation_p.A54T|MARCH2_ENST00000601283.1_Intron|RP11-886P16.6_ENST00000595706.1_RNA|MARCH2_ENST00000215555.2_Missense_Mutation_p.A54T			Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2, E3 ubiquitin protein ligase	54			A -> T (in dbSNP:rs1133893). {ECO:0000269|PubMed:15489334}.		endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|skin(1)|urinary_tract(1)	10						CGTCATCCGTGCCTTGGACAC	0.607													G|||	996	0.198882	0.0348	0.2723	5008	,	,		18467	0.2381		0.2922	False		,,,				2504	0.2321																0								G	THR/ALA,THR/ALA,THR/ALA	420,3986	204.1+/-226.4	23,374,1806	87.0	69.0	75.0		160,160,160	4.6	1.0	19	dbSNP_86	75	2872,5728	450.7+/-362.5	470,1932,1898	yes	missense,missense,missense	MARCH2	NM_001005415.1,NM_001005416.1,NM_016496.4	58,58,58	493,2306,3704	AA,AG,GG		33.3953,9.5325,25.3114	benign,benign,benign	54/247,54/177,54/247	8486884	3292,9714	2203	4300	6503	SO:0001583	missense	51257			AF151074	CCDS12202.1, CCDS32894.1	19p13.2	2013-01-09	2012-02-23			ENSG00000099785		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	28038	protein-coding gene	gene with protein product		613332	"""membrane-associated ring finger (C3HC4) 2"""			11042152, 14722266	Standard	NM_016496		Approved	HSPC240, MARCH-II, RNF172	uc002mjw.3	Q9P0N8		ENST00000602117.1:c.160G>A	19.37:g.8486884G>A	ENSP00000471536:p.Ala54Thr	Somatic		WXS	SOLID	Phase_I	A6NP10|Q5H785|Q8N5A3|Q96B78	Missense_Mutation	SNP	ENST00000602117.1	37	CCDS12202.1	476	0.21794871794871795	22	0.044715447154471545	109	0.3011049723756906	124	0.21678321678321677	221	0.29155672823219	G	14.98	2.696507	0.48202	0.095325	0.333953	ENSG00000099785	ENST00000393944;ENST00000215555;ENST00000381035	T;T;T	0.15017	2.46;2.46;2.46	5.65	4.6	0.57074	.	0.109437	0.64402	D	0.000010	T	0.00012	0.0000	L	0.52364	1.645	0.19775	P	0.999951435	B;B	0.30851	0.05;0.297	B;B	0.33890	0.073;0.172	T	0.46233	-0.9206	9	0.13853	T	0.58	-19.541	14.7238	0.69329	0.0:0.0:0.854:0.146	rs1133893;rs3196037;rs11540064;rs11882865;rs17352509;rs17846004;rs17858988;rs58815990;rs11882865	54;54	Q9P0N8-2;Q9P0N8	.;MARH2_HUMAN	T	54	ENSP00000377518:A54T;ENSP00000215555:A54T;ENSP00000370423:A54T	ENSP00000215555:A54T	A	+	1	0	MARCH2	8392884	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.156000	0.58138	1.362000	0.46000	0.555000	0.69702	GCC		0.607	MARCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460361.2		NM_016496	
NBPF7	343505	hgsc.bcm.edu	37	1	120384017	120384017	+	IGR	SNP	A	A	T			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr1:120384017A>T								REG4 (29734 upstream) : ADAM30 (52138 downstream)																							ACCTGGGCTGAGCTTGTGGAC	0.577																																																	0													73.0	79.0	77.0					1																	120384017		2203	4300	6503	SO:0001628	intergenic_variant	343505																															1.37:g.120384017A>T		Somatic		WXS	SOLID	Phase_I		Missense_Mutation	SNP		37																																																																																				0	0.577									
NKG7	4818	hgsc.bcm.edu	37	19	51875304	51875304	+	Missense_Mutation	SNP	G	G	A	rs370793095		TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr19:51875304G>A	ENST00000221978.5	-	3	508	c.329C>T	c.(328-330)gCg>gTg	p.A110V	NKG7_ENST00000595217.1_Missense_Mutation_p.R104W|NKG7_ENST00000600427.1_Intron	NM_005601.3	NP_005592.1	Q16617	NKG7_HUMAN	natural killer cell granule protein 7	110						integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GGTGTACACCGCCATGGCCAC	0.617																																																	0								G	VAL/ALA	0,4406		0,0,2203	57.0	62.0	60.0		329	0.8	0.0	19		60	1,8599	1.2+/-3.3	0,1,4299	no	missense	NKG7	NM_005601.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	110/166	51875304	1,13005	2203	4300	6503	SO:0001583	missense	4818				CCDS12830.1	19q13.41	2014-03-07	2014-03-07		ENSG00000105374	ENSG00000105374			7830	protein-coding gene	gene with protein product	"""granule membrane protein 17"""	606008	"""natural killer cell group 7 sequence"""			8458737	Standard	NM_005601		Approved	GIG1, GMP-17	uc002pwj.3	Q16617	OTTHUMG00000182898	ENST00000221978.5:c.329C>T	19.37:g.51875304G>A	ENSP00000221978:p.Ala110Val	Somatic		WXS	SOLID	Phase_I		Missense_Mutation	SNP	ENST00000221978.5	37	CCDS12830.1	.	.	.	.	.	.	.	.	.	.	G	8.484	0.860560	0.17178	0.0	1.16E-4	ENSG00000105374	ENST00000221978	T	0.09723	2.95	5.65	0.757	0.18427	.	1.172550	0.06292	N	0.699352	T	0.08714	0.0216	L	0.38175	1.15	0.18873	N	0.999985	B	0.21452	0.056	B	0.21360	0.034	T	0.40776	-0.9545	10	0.05525	T	0.97	-0.5276	10.5423	0.45039	0.1937:0.0:0.8063:0.0	.	110	Q16617	NKG7_HUMAN	V	110	ENSP00000221978:A110V	ENSP00000221978:A110V	A	-	2	0	NKG7	56567116	0.001000	0.12720	0.022000	0.16811	0.165000	0.22458	0.022000	0.13511	-0.024000	0.13941	0.491000	0.48974	GCG		0.617	NKG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464260.2		NM_005601	
QSER1	79832	hgsc.bcm.edu	37	11	32956639	32956639	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr11:32956639A>C	ENST00000399302.2	+	4	3783	c.3448A>C	c.(3448-3450)Att>Ctt	p.I1150L	QSER1_ENST00000527788.1_Missense_Mutation_p.I911L	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1150										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AACAGGATTTATTGCTTCTTT	0.438																																																	0													82.0	81.0	81.0					11																	32956639		1852	4090	5942	SO:0001583	missense	79832			AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.3448A>C	11.37:g.32956639A>C	ENSP00000382241:p.Ile1150Leu	Somatic		WXS	SOLID	Phase_I	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	37	CCDS41631.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.03|14.03	2.414242|2.414242	0.42817|0.42817	.|.	.|.	ENSG00000060749|ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788|ENST00000524678	T;T|.	0.25579|.	2.11;1.79|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.000000|.	0.64402|.	D|.	0.000002|.	T|T	0.70272|0.70272	0.3205|0.3205	L|L	0.57536|0.57536	1.79|1.79	0.50039|0.50039	D|D	0.999849|0.999849	D;P;P|.	0.62365|.	0.991;0.504;0.603|.	D;B;B|.	0.72625|.	0.978;0.425;0.089|.	T|T	0.68957|0.68957	-0.5272|-0.5272	10|5	0.54805|.	T|.	0.06|.	.|.	15.5209|15.5209	0.75866|0.75866	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	911;911;1150|.	C9JJ88;Q2KHR3-2;Q2KHR3|.	.;.;QSER1_HUMAN|.	L|F	1150;911;911|170	ENSP00000382241:I1150L;ENSP00000432766:I911L|.	ENSP00000078652:I911L|.	I|L	+|+	1|3	0|2	QSER1|QSER1	32913215|32913215	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	4.716000|4.716000	0.61916|0.61916	2.073000|2.073000	0.62155|0.62155	0.383000|0.383000	0.25322|0.25322	ATT|TTA		0.438	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1		NM_024774	
TCF3	6929	hgsc.bcm.edu	37	19	1650219	1650219	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr19:1650219A>G	ENST00000262965.5	-	2	373	c.29T>C	c.(28-30)gTg>gCg	p.V10A	TCF3_ENST00000344749.5_Missense_Mutation_p.V10A|TCF3_ENST00000588136.1_Missense_Mutation_p.V10A|TCF3_ENST00000395423.3_Missense_Mutation_p.V10A	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0	CTNNB1-binding. {ECO:0000250}.|Gly-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTCTGTGCCCACAGGCGCCAT	0.652			T	"""PBX1, HLF, TFPT"""	pre B-ALL																																			Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	0													36.0	38.0	37.0					19																	1650219		2179	4260	6439	SO:0001583	missense	6929			M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"""Basic helix-loop-helix proteins"""	11633	protein-coding gene	gene with protein product	"""transcription factor E2-alpha"", ""immunoglobulin transcription factor 1"", ""kappa-E2-binding factor"", ""E2A immunoglobulin enhancer-binding factor E12/E47"", ""VDR interacting repressor"""	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.29T>C	19.37:g.1650219A>G	ENSP00000262965:p.Val10Ala	Somatic		WXS	SOLID	Phase_I	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000262965.5	37	CCDS12074.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.570980	0.45798	.	.	ENSG00000071564	ENST00000262965;ENST00000344749;ENST00000453954;ENST00000395423	T;T;T	0.54479	2.17;2.18;0.57	4.13	3.08	0.35506	.	0.146862	0.45361	D	0.000374	T	0.60856	0.2301	L	0.49350	1.555	0.42033	D	0.991033	B;D;P	0.64830	0.047;0.994;0.714	B;D;B	0.70716	0.036;0.97;0.267	T	0.61237	-0.7103	10	0.51188	T	0.08	4.2549	7.8491	0.29444	0.8952:0.0:0.1048:0.0	.	10;10;10	P15923-2;P15923;Q2TB39	.;TFE2_HUMAN;.	A	10	ENSP00000262965:V10A;ENSP00000344375:V10A;ENSP00000378813:V10A	ENSP00000262965:V10A	V	-	2	0	TCF3	1601219	1.000000	0.71417	0.884000	0.34674	0.957000	0.61999	4.411000	0.59781	1.729000	0.51567	0.379000	0.24179	GTG		0.652	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1		NM_003200	
THOC3	84321	hgsc.bcm.edu	37	5	175388335	175388335	+	Silent	SNP	T	T	C	rs201011758		TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr5:175388335T>C	ENST00000265097.4	-	4	822	c.732A>G	c.(730-732)gcA>gcG	p.A244A	THOC3_ENST00000513482.1_Silent_p.A244A|THOC3_ENST00000510300.1_5'UTR|RP11-91H12.4_ENST00000502813.1_RNA|THOC3_ENST00000514861.1_Silent_p.A59A	NM_032361.2	NP_115737.1	Q96J01	THOC3_HUMAN	THO complex 3	244					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)	4	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		CCAAAGCATCTGCACTTCCTG	0.493																																																	0													15.0	13.0	14.0					5																	175388335		1113	1915	3028	SO:0001819	synonymous_variant	84321			BC006849	CCDS4397.1	5q35.3	2013-02-11			ENSG00000051596	ENSG00000051596		"""WD repeat domain containing"", ""THO complex subunits"""	19072	protein-coding gene	gene with protein product		606929				11979277	Standard	NM_032361		Approved	TEX1, MGC5469	uc003mdg.5	Q96J01	OTTHUMG00000130658	ENST00000265097.4:c.732A>G	5.37:g.175388335T>C		Somatic		WXS	SOLID	Phase_I	Q6NZ53	Silent	SNP	ENST00000265097.4	37	CCDS4397.1	248	0.11355311355311355	56	0.11382113821138211	47	0.1298342541436464	32	0.055944055944055944	113	0.14907651715039577	T	10.68	1.417318	0.25552	.	.	ENSG00000051596	ENST00000505969	.	.	.	4.74	-8.0	0.01126	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	0.9999999999999427	.	.	.	.	.	.	T	0.17992	-1.0351	3	.	.	.	-11.9501	6.3489	0.21365	0.2591:0.4233:0.0:0.3176	.	.	.	.	G	28	.	.	R	-	1	2	THOC3	175320941	0.002000	0.14202	0.959000	0.39883	0.990000	0.78478	-1.500000	0.02283	-0.895000	0.03920	-0.509000	0.04479	AGA		0.493	THOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253148.1			
ZNF521	25925	hgsc.bcm.edu	37	18	22806401	22806401	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr18:22806401T>C	ENST00000361524.3	-	4	1629	c.1481A>G	c.(1480-1482)gAa>gGa	p.E494G	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.E274G|ZNF521_ENST00000538137.2_Missense_Mutation_p.E494G	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	494					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TCGGATGTGTTCCTGAAGAGT	0.463			T	PAX5	ALL																																			Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0													101.0	100.0	100.0					18																	22806401		2203	4300	6503	SO:0001583	missense	25925			AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.1481A>G	18.37:g.22806401T>C	ENSP00000354794:p.Glu494Gly	Somatic		WXS	SOLID	Phase_I	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	T	11.22	1.574763	0.28092	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.28666	1.6;1.6	6.06	6.06	0.98353	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.048029	0.85682	D	0.000000	T	0.33904	0.0879	L	0.32530	0.975	0.42219	D	0.991843	P	0.49862	0.929	P	0.49451	0.611	T	0.02829	-1.1105	10	0.31617	T	0.26	-22.3395	16.2741	0.82634	0.0:0.0:0.0:1.0	.	494	Q96K83	ZN521_HUMAN	G	494;528;494	ENSP00000354794:E494G;ENSP00000382352:E494G	ENSP00000354794:E494G	E	-	2	0	ZNF521	21060399	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.673000	0.83973	2.322000	0.78497	0.528000	0.53228	GAA		0.463	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2		NM_015461	
ZNF717	100131827	hgsc.bcm.edu	37	3	75787812	75787813	+	Frame_Shift_Ins	INS	-	-	T	rs138918118|rs143242394		TCGA-CJ-4890-01A-01D-1373-10	TCGA-CJ-4890-11A-01D-1373-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2e4289bf-7d28-419b-9f31-9633a203bfd4	090c84e4-4034-4a08-81ea-d6650fe28373	g.chr3:75787812_75787813insT	ENST00000478296.1	-	4	1087_1088	c.811_812insA	c.(811-813)agcfs	p.S271fs	ZNF717_ENST00000491507.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000422325.1_Frame_Shift_Ins_p.S321fs|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.S314fs|ZNF717_ENST00000477374.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	314					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GGACTTATAGCTGAACAATTTT	0.426																																																	0										368,754		140,88,333						-3.2	0.0		dbSNP_130	5	819,1629		327,165,732	no	frameshift	ZNF717	NM_001128223.1		467,253,1065	A1A1,A1R,RR		33.4559,32.7986,33.2493				1187,2383				SO:0001589	frameshift_variant	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.812dupA	3.37:g.75787813_75787813dupT	ENSP00000419377:p.Ser271fs	Somatic		WXS	SOLID	Phase_I		Frame_Shift_Ins	INS	ENST00000478296.1	37																																																																																					0.426	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2		NM_001128223	
