#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_CAF	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
CA5B	11238	genome.wustl.edu	37	X	15790686	15790686	+	Missense_Mutation	SNP	C	C	G			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chrX:15790686C>G	ENST00000318636.3	+	4	544	c.408C>G	c.(406-408)atC>atG	p.I136M	CA5B_ENST00000454127.2_Missense_Mutation_p.I136M	NM_007220.3	NP_009151.1	Q8WTZ4	CA5BL_HUMAN	carbonic anhydrase VB, mitochondrial	90						mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)|prostate(1)|stomach(2)	9	Hepatocellular(33;0.183)					GGGGGGCCATCGATGCCTGGG	0.507																																							0											0													171.0	154.0	160.0					X																	15790686		2203	4300	6503	SO:0001583	missense	0			AB021660	CCDS14171.1	Xp22.1	2008-08-13			ENSG00000169239	ENSG00000169239		"""Carbonic anhydrases"""	1378	protein-coding gene	gene with protein product		300230				10409679	Standard	XM_005274442		Approved		uc004cxe.3	Q9Y2D0	OTTHUMG00000021183	ENST00000318636.3:c.408C>G	X.37:g.15790686C>G	ENSP00000314099:p.Ile136Met		A6NEZ4	Missense_Mutation	SNP	pfam_Carbonic_anhydrase_a,superfamily_Carbonic_anhydrase_a,pfscan_Carbonic_anhydrase_a	p.I136M	ENST00000318636.3	37	c.408	CCDS14171.1	X	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967038	0.53507	.	.	ENSG00000169239	ENST00000318636;ENST00000479740;ENST00000454127	T;T;T	0.67171	-0.24;-0.25;-0.24	5.6	-9.18	0.00688	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.149412	0.64402	D	0.000008	T	0.59211	0.2177	N	0.22421	0.69	0.09310	N	0.99999	D	0.63880	0.993	D	0.65987	0.94	T	0.68443	-0.5407	10	0.48119	T	0.1	-18.4968	11.1246	0.48310	0.1019:0.2469:0.0:0.6512	.	136	Q9Y2D0	CAH5B_HUMAN	M	136	ENSP00000314099:I136M;ENSP00000417553:I136M;ENSP00000417021:I136M	ENSP00000314099:I136M	I	+	3	3	CA5B	15700607	0.004000	0.15560	0.388000	0.26195	0.979000	0.70002	-1.128000	0.03247	-2.116000	0.00830	-0.853000	0.03031	ATC	0	pfam_Carbonic_anhydrase_a,superfamily_Carbonic_anhydrase_a,pfscan_Carbonic_anhydrase_a		0.507	CA5B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	CA5B	protein_coding	OTTHUMT00000354933.1	30	117	0	0.00	0	0	C	NM_007220	0	0		15790686	1	no_errors	ENST00000318636	ensembl	human	known	74_37	missense	5	22	75	81.36	15	96	SNP	0.02	G
MTMR8	55613	genome.wustl.edu	37	X	63488809	63488809	+	Missense_Mutation	SNP	T	T	G			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chrX:63488809T>G	ENST00000374852.3	-	14	1790	c.1723A>C	c.(1723-1725)Atc>Ctc	p.I575L	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	575						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TCTCCATTGATACCCATAAAG	0.488																																							0											2	Whole gene deletion(2)	ovary(1)|large_intestine(1)											75.0	63.0	67.0					X																	63488809		2203	4300	6503	SO:0001583	missense	0			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1723A>C	X.37:g.63488809T>G	ENSP00000363985:p.Ile575Leu		Q5JT99|Q9NXP6	Missense_Mutation	SNP	pfam_Myotubularin-like_Pase_dom,smart_Tyr_Pase_cat	p.I575L	ENST00000374852.3	37	c.1723	CCDS14379.1	X	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.922|9.922	1.212519|1.212519	0.22289|0.22289	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000374852;ENST00000247400|ENST00000442913	D|.	0.94330|.	-3.4|.	2.6|2.6	0.198|0.198	0.15168|0.15168	.|.	0.351810|.	0.17952|.	U|.	0.156474|.	T|T	0.15089|0.15089	0.0364|0.0364	N|N	0.08118|0.08118	0|0	0.22446|0.22446	N|N	0.999093|0.999093	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.26883|0.26883	-1.0090|-1.0090	10|5	0.21014|.	T|.	0.42|.	.|.	4.2507|4.2507	0.10693|0.10693	0.0:0.3585:0.0:0.6415|0.0:0.3585:0.0:0.6415	.|.	575|.	Q96EF0|.	MTMR8_HUMAN|.	L|S	575;461|378	ENSP00000363985:I575L|.	ENSP00000247400:I461L|.	I|Y	-|-	1|2	0|0	MTMR8|MTMR8	63405534|63405534	0.312000|0.312000	0.24545|0.24545	0.227000|0.227000	0.23927|0.23927	0.973000|0.973000	0.67179|0.67179	0.317000|0.317000	0.19487|0.19487	-0.039000|-0.039000	0.13602|0.13602	0.430000|0.430000	0.28490|0.28490	ATC|TAT	0	NULL		0.488	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTMR8	protein_coding	OTTHUMT00000056949.2	26	103	0	0.00	0	0	T	NM_017677	0	0		63488809	-1	no_errors	ENST00000374852	ensembl	human	known	74_37	missense	1	27	88.89	43.75	8	21	SNP	0.229	G
VWA5B1	127731	genome.wustl.edu	37	1	20640980	20640980	+	Missense_Mutation	SNP	C	C	T	rs374632705		TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr1:20640980C>T	ENST00000375079.2	+	4	654	c.458C>T	c.(457-459)aCg>aTg	p.T153M	RP4-745E8.2_ENST00000444923.1_RNA|VWA5B1_ENST00000289815.8_Missense_Mutation_p.T153M|VWA5B1_ENST00000375083.4_Missense_Mutation_p.T153M|VWA5B1_ENST00000289825.4_5'UTR	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	153						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GAGCTCCCAACGCTGCCCAGC	0.622																																							0											0													42.0	42.0	42.0					1																	20640980		692	1591	2283	SO:0001583	missense	0			AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.458C>T	1.37:g.20640980C>T	ENSP00000364220:p.Thr153Met		A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	pfam_VWF_A,smart_VWF_A,pfscan_VWF_A	p.T153M	ENST00000375079.2	37	c.458		1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647275	0.87958	.	.	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000375079	T;T;T	0.06933	3.57;3.24;3.56	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.33381	0.0861	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.03945	-1.0990	10	0.87932	D	0	-10.8229	18.1375	0.89624	0.0:1.0:0.0:0.0	.	153;153	Q5TIE3;Q5TIE3-2	VW5B1_HUMAN;.	M	153	ENSP00000289815:T153M;ENSP00000364224:T153M;ENSP00000364220:T153M	ENSP00000289815:T153M	T	+	2	0	VWA5B1	20513567	1.000000	0.71417	0.255000	0.24374	0.858000	0.48976	5.579000	0.67457	2.647000	0.89833	0.467000	0.42956	ACG	0	NULL		0.622	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	VWA5B1	protein_coding	OTTHUMT00000007945.4	63	126	0	0.00	0	0	C	XM_001722222	rs374632705	C->T		20640980	1	no_errors	ENST00000289815	ensembl	human	known	74_37	missense	27	75	38.64	37.50	17	45	SNP	0.993	T
CLASP1	23332	genome.wustl.edu	37	2	122165068	122165068	+	Missense_Mutation	SNP	A	A	G			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr2:122165068A>G	ENST00000263710.4	-	25	3037	c.2648T>C	c.(2647-2649)cTg>cCg	p.L883P	CLASP1_ENST00000397587.3_Missense_Mutation_p.L863P|CLASP1_ENST00000455322.2_Missense_Mutation_p.L855P|CLASP1_ENST00000541859.1_Missense_Mutation_p.L616P|CLASP1_ENST00000545861.1_Missense_Mutation_p.L630P|CLASP1_ENST00000541377.1_Missense_Mutation_p.L861P|CLASP1_ENST00000409078.3_Missense_Mutation_p.L855P	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	883					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					TTGGCTCTTCAGTAAGTTCTG	0.458																																							0											0													67.0	64.0	65.0					2																	122165068		1879	4111	5990	SO:0001583	missense	0			AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2648T>C	2.37:g.122165068A>G	ENSP00000263710:p.Leu883Pro		B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	pfam_CLASP_N_dom,pfam_HEAT,superfamily_ARM-type_fold,pfscan_HEAT_type_2	p.L883P	ENST00000263710.4	37	c.2648		2	.	.	.	.	.	.	.	.	.	.	A	26.9	4.777622	0.90195	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41	6.06	6.06	0.98353	Armadillo-like helical (1);Armadillo-type fold (1);	0.059166	0.64402	D	0.000002	T	0.79581	0.4470	L	0.58101	1.795	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.998;0.998	D;D;D;D	0.74348	0.964;0.971;0.973;0.983	T	0.81174	-0.1053	10	0.87932	D	0	-36.21	16.6127	0.84892	1.0:0.0:0.0:0.0	.	855;863;861;883	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	P	883;855;863;861;616;855;630	ENSP00000263710:L883P;ENSP00000389372:L855P;ENSP00000380717:L863P;ENSP00000441625:L861P;ENSP00000441770:L616P;ENSP00000386442:L855P;ENSP00000438620:L630P	ENSP00000263710:L883P	L	-	2	0	CLASP1	121881538	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	8.930000	0.92872	2.322000	0.78497	0.528000	0.53228	CTG	0	superfamily_ARM-type_fold		0.458	CLASP1-201	KNOWN	basic	protein_coding	CLASP1	protein_coding		57	165	0	0.00	0	0	A	NM_015282	0	0		122165068	-1	no_errors	ENST00000263710	ensembl	human	known	74_37	missense	37	165	36.21	36.78	21	96	SNP	1	G
NR1I2	8856	genome.wustl.edu	37	3	119534625	119534625	+	Silent	SNP	C	C	T	rs369188703		TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr3:119534625C>T	ENST00000337940.4	+	8	1272	c.1224C>T	c.(1222-1224)ttC>ttT	p.F408F	NR1I2_ENST00000466380.1_Silent_p.F332F|NR1I2_ENST00000393716.2_Silent_p.F369F	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	369	Ligand-binding.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	AGGAGCAATTCGCCATTACTC	0.602																																							0											0								T	,,	0,4406		0,0,2203	56.0	51.0	52.0		1107,1224,996	-5.3	0.0	3		52	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	NR1I2	NM_003889.3,NM_022002.2,NM_033013.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	369/435,408/474,332/398	119534625	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	0			AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"""Nuclear hormone receptors"""	7968	protein-coding gene	gene with protein product	"""pregnane X receptor"", ""orphan nuclear receptor PXR"""	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.1224C>T	3.37:g.119534625C>T			Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	pfam_Nucl_hrmn_rcpt_lig-bd_core,pfam_Znf_hrmn_rcpt,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,prints_Str_hrmn_rcpt,prints_Znf_hrmn_rcpt,pfscan_Znf_hrmn_rcpt	p.F408	ENST00000337940.4	37	c.1224	CCDS2995.1	3																																																																																			0	pfam_Nucl_hrmn_rcpt_lig-bd_core,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Nucl_hrmn_rcpt_lig-bd_core		0.602	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NR1I2	protein_coding	OTTHUMT00000355126.1	39	119	0	0.00	0	0	C		rs369188703	C->T		119534625	1	no_errors	ENST00000337940	ensembl	human	known	74_37	silent	16	80	33.33	40.44	8	55	SNP	0	T
PEX5L	51555	genome.wustl.edu	37	3	179519473	179519473	+	3'UTR	SNP	A	A	C			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr3:179519473A>C	ENST00000467460.1	-	0	2354				PEX5L_ENST00000263962.8_3'UTR|PEX5L_ENST00000476138.1_3'UTR|PEX5L_ENST00000467440.2_5'UTR|PEX5L_ENST00000468741.1_3'UTR|PEX5L_ENST00000392649.3_3'UTR|PEX5L_ENST00000485199.1_3'UTR|PEX5L_ENST00000472994.1_3'UTR|RP11-494H4.3_ENST00000602704.1_lincRNA	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like						maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			GGCATTGTCCACAGGAATTAA	0.328																																							0											0																																										SO:0001624	3_prime_UTR_variant	0			AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"""Tetratricopeptide (TTC) repeat domain containing"""	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.*143T>G	3.37:g.179519473A>C			B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	RNA	SNP	0	NULL	ENST00000467460.1	37	NULL	CCDS3236.1	3																																																																																			0	0		0.328	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PEX5L	protein_coding	OTTHUMT00000348577.1	81	183	0	0.00	0	0	A	NM_016559	0	0		179519473	-1	no_errors	ENST00000467440	ensembl	human	known	74_37	rna	53	145	41.11	36.96	37	85	SNP	0.002	C
ADAM29	11086	genome.wustl.edu	37	4	175897904	175897904	+	Nonsense_Mutation	SNP	G	G	T			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr4:175897904G>T	ENST00000359240.3	+	5	1898	c.1228G>T	c.(1228-1230)Gag>Tag	p.E410*	ADAM29_ENST00000514159.1_Nonsense_Mutation_p.E410*|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Nonsense_Mutation_p.E410*|ADAM29_ENST00000404450.4_Nonsense_Mutation_p.E410*	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	410	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		AGAAGGAGAAGAGTGTGACTG	0.423																																					Ovarian(140;1727 1835 21805 25838 41440)		0											0													254.0	242.0	246.0					4																	175897904		2203	4300	6503	SO:0001587	stop_gained	0			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1228G>T	4.37:g.175897904G>T	ENSP00000352177:p.Glu410*		Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Nonsense_Mutation	SNP	pfam_Peptidase_M12B,pfam_ADAM_Cys-rich,pfam_Peptidase_M12B_N,pfam_Blood-coag_inhib_Disintegrin,superfamily_Blood-coag_inhib_Disintegrin,smart_Blood-coag_inhib_Disintegrin,smart_ADAM_Cys-rich,pfscan_Blood-coag_inhib_Disintegrin,pfscan_Peptidase_M12B,prints_Blood-coag_inhib_Disintegrin	p.E410*	ENST00000359240.3	37	c.1228	CCDS3823.1	4	.	.	.	.	.	.	.	.	.	.	G	37	6.227759	0.97394	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	.	.	.	3.6	-0.646	0.11472	.	0.226223	0.21249	U	0.077680	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2974	0.66325	0.0:0.589:0.4109:0.0	.	.	.	.	X	410	.	.	E	+	1	0	ADAM29	176134479	0.558000	0.26554	0.005000	0.12908	0.026000	0.11368	-0.343000	0.07791	-0.156000	0.11079	-0.302000	0.09304	GAG	0	pfam_Blood-coag_inhib_Disintegrin,superfamily_Blood-coag_inhib_Disintegrin,smart_Blood-coag_inhib_Disintegrin,pfscan_Blood-coag_inhib_Disintegrin		0.423	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	ADAM29	protein_coding		40	134	2.38	0.00	1	0	G		0	0		175897904	1	no_errors	ENST00000359240	ensembl	human	known	74_37	nonsense	23	122	55.77	44.80	29	99	SNP	0.053	T
MCC	4163	genome.wustl.edu	37	5	112384918	112384918	+	Missense_Mutation	SNP	G	G	A	rs139015770		TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr5:112384918G>A	ENST00000302475.4	-	14	2520	c.1957C>T	c.(1957-1959)Cgg>Tgg	p.R653W	MCC_ENST00000408903.3_Missense_Mutation_p.R843W|MCC_ENST00000515367.2_Missense_Mutation_p.R590W|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	653					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		TGGGCCTCCCGCGTGCTCAGC	0.602																																							0											0								G	TRP/ARG,TRP/ARG	1,4403	2.1+/-5.4	0,1,2201	52.0	40.0	44.0		2527,1957	4.0	1.0	5	dbSNP_134	44	0,8600		0,0,4300	no	missense,missense	MCC	NM_001085377.1,NM_002387.2	101,101	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	843/1020,653/830	112384918	1,13003	2202	4300	6502	SO:0001583	missense	0				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1957C>T	5.37:g.112384918G>A	ENSP00000305617:p.Arg653Trp		D3DT05|Q6ZR04	Missense_Mutation	SNP	pfam_USH1C-bd_PDZ_domain,superfamily_tRNA-bd_arm	p.R653W	ENST00000302475.4	37	c.1957	CCDS4111.1	5	.	.	.	.	.	.	.	.	.	.	G	22.0	4.228147	0.79576	2.27E-4	0.0	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.36340	2.43;2.43;1.26	4.87	3.96	0.45880	.	0.000000	0.64402	D	0.000002	T	0.41096	0.1144	N	0.14661	0.345	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.973;0.992;0.973	T	0.29274	-1.0017	10	0.35671	T	0.21	-22.5143	13.9618	0.64185	0.0:0.0:0.8422:0.1578	.	653;843;653	B7Z6G0;P23508-2;P23508	.;.;CRCM_HUMAN	W	653;590;843	ENSP00000305617:R653W;ENSP00000421615:R590W;ENSP00000386227:R843W	ENSP00000305617:R653W	R	-	1	2	MCC	112412817	1.000000	0.71417	0.991000	0.47740	0.983000	0.72400	4.832000	0.62759	0.966000	0.38159	0.462000	0.41574	CGG	0	NULL		0.602	MCC-001	KNOWN	basic|CCDS	protein_coding	MCC	protein_coding	OTTHUMT00000250736.3	43	88	0	0.00	0	0	G	NM_001085377	rs139015770	G->A		112384918	-1	no_errors	ENST00000302475	ensembl	human	known	74_37	missense	25	86	19.35	4.44	6	4	SNP	1	A
SCAF8	22828	genome.wustl.edu	37	6	155153402	155153402	+	Missense_Mutation	SNP	C	C	G			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr6:155153402C>G	ENST00000367178.3	+	20	3265	c.2689C>G	c.(2689-2691)Ctg>Gtg	p.L897V	SCAF8_ENST00000417268.1_Missense_Mutation_p.L897V|SCAF8_ENST00000367186.4_Missense_Mutation_p.L963V|TIAM2_ENST00000461783.3_5'Flank	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	897	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						TCCTGGACTTCTGGGAACACA	0.458																																							0											0													107.0	112.0	111.0					6																	155153402		2203	4300	6503	SO:0001583	missense	0			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.2689C>G	6.37:g.155153402C>G	ENSP00000356146:p.Leu897Val		B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	pfam_RNA_pol_II-bd,pfam_RRM_dom,superfamily_ENTH_VHS,smart_CID_dom,smart_RRM_dom,pfscan_RRM_dom	p.L963V	ENST00000367178.3	37	c.2887	CCDS5247.1	6	.	.	.	.	.	.	.	.	.	.	C	10.71	1.426957	0.25726	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.51817	0.7;0.7;0.69	5.58	1.91	0.25777	.	0.101689	0.38959	U	0.001520	T	0.22166	0.0534	L	0.56769	1.78	0.34652	D	0.721783	P;P;P	0.47350	0.802;0.802;0.894	B;B;B	0.43950	0.277;0.277;0.437	T	0.05321	-1.0892	10	0.27082	T	0.32	.	2.7618	0.05308	0.3299:0.2874:0.0:0.3827	.	942;963;897	B7Z876;B7Z888;Q9UPN6	.;.;SCAF8_HUMAN	V	897;897;963	ENSP00000356146:L897V;ENSP00000413098:L897V;ENSP00000356154:L963V	ENSP00000356146:L897V	L	+	1	2	SCAF8	155195094	0.583000	0.26757	1.000000	0.80357	0.999000	0.98932	0.515000	0.22801	0.397000	0.25310	0.655000	0.94253	CTG	0	NULL		0.458	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCAF8	protein_coding	OTTHUMT00000042798.1	49	184	0	0.00	0	0	C	NM_014892	0	0		155153402	1	no_errors	ENST00000367186	ensembl	human	known	74_37	missense	27	157	46	45.14	23	130	SNP	0.996	G
GTF2I	2969	genome.wustl.edu	37	7	74146970	74146970	+	Missense_Mutation	SNP	T	T	A			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr7:74146970T>A	ENST00000324896.4	+	15	1660	c.1271T>A	c.(1270-1272)cTt>cAt	p.L424H	GTF2I_ENST00000346152.4_Missense_Mutation_p.L403H|GTF2I_ENST00000416070.1_Missense_Mutation_p.L383H|GTF2I_ENST00000353920.4_Missense_Mutation_p.L404H	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	424					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						AGGATATTACTTGCAAAGGAA	0.378																																							0											0													13.0	13.0	13.0					7																	74146970		1741	3768	5509	SO:0001583	missense	0			U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.1271T>A	7.37:g.74146970T>A	ENSP00000322542:p.Leu424His		O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I	p.L424H	ENST00000324896.4	37	c.1271	CCDS5573.1	7	.	.	.	.	.	.	.	.	.	.	T	18.18	3.565904	0.65651	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.72	4.72	0.59763	.	0.110120	0.39544	N	0.001322	T	0.37019	0.0988	N	0.14661	0.345	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;0.999	D;D;P;D;D	0.74348	0.983;0.979;0.874;0.971;0.963	T	0.36089	-0.9762	10	0.56958	D	0.05	-16.5588	13.3771	0.60745	0.0:0.0:0.0:1.0	.	402;383;404;403;424	Q499G6;P78347-2;P78347-3;P78347-4;P78347	.;.;.;.;GTF2I_HUMAN	H	424;419;404;403;383	ENSP00000322542:L424H;ENSP00000322671:L404H;ENSP00000322599:L403H;ENSP00000387651:L383H	ENSP00000322542:L424H	L	+	2	0	GTF2I	73784906	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.342000	0.65970	1.753000	0.51906	0.477000	0.44152	CTT	0	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I		0.378	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GTF2I	protein_coding	OTTHUMT00000252708.1	346	62	0	0.00	0	0	T	NM_032999	0	0		74146970	1	no_errors	ENST00000324896	ensembl	human	known	74_37	missense	206	69	39.65	44.35	136	55	SNP	1	A
NUDT5	11164	genome.wustl.edu	37	10	12211342	12211342	+	Intron	SNP	G	G	A	rs376483075	byFrequency	TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr10:12211342G>A	ENST00000491614.1	-	9	946				SEC61A2_ENST00000495368.1_3'UTR|SEC61A2_ENST00000304267.8_3'UTR|NUDT5_ENST00000378937.3_Intron|NUDT5_ENST00000537776.1_Intron|NUDT5_ENST00000378952.3_Intron			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5						D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				AACCCCGCACGGCATTTCACA	0.453													g|||	4	0.000798722	0.003	0.0	5008	,	,		19218	0.0		0.0	False		,,,				2504	0.0						0											0								A	,	4,3096		0,4,1546	46.0	38.0	41.0		,	-1.3	0.0	10		41	0,7058		0,0,3529	no	utr-3,intron	NUDT5,SEC61A2	NM_001142627.1,NM_014142.2	,	0,4,5075	AA,AG,GG		0.0,0.129,0.0394	,	,	12211342	4,10154	1550	3529	5079	SO:0001627	intron_variant	0			AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.550+1373C>T	10.37:g.12211342G>A			A8K516|Q6IAG0|Q9UH49	RNA	SNP	0	NULL	ENST00000491614.1	37	NULL	CCDS7089.1	10																																																																																			0	0		0.453	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEC61A2	protein_coding	OTTHUMT00000046811.1	38	229	0	0.00	0	0	G		rs376483075	G->A		12211342	1	no_errors	ENST00000495368	ensembl	human	known	74_37	rna	26	182	29.73	41.29	11	128	SNP	0	A
OR5M9	390162	genome.wustl.edu	37	11	56230566	56230566	+	Silent	SNP	G	G	A			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr11:56230566G>A	ENST00000279791.1	-	1	311	c.312C>T	c.(310-312)gcC>gcT	p.A104A		NM_001004743.1	NP_001004743.1	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M, member 9	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A104A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	36	Esophageal squamous(21;0.00448)					CGTGGACAACGGCAATGAAAA	0.473																																							0											1	Substitution - coding silent(1)	lung(1)											127.0	119.0	122.0					11																	56230566		2201	4296	6497	SO:0001819	synonymous_variant	0			AB065747	CCDS31531.1	11q11	2012-08-09			ENSG00000150269	ENSG00000150269		"""GPCR / Class A : Olfactory receptors"""	15294	protein-coding gene	gene with protein product							Standard	NM_001004743		Approved		uc010rjj.2	Q8NGP3	OTTHUMG00000166874	ENST00000279791.1:c.312C>T	11.37:g.56230566G>A			Q6IEW5|Q96RB9	Silent	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.A104	ENST00000279791.1	37	c.312	CCDS31531.1	11																																																																																			0	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_GPCR_Rhodpsn		0.473	OR5M9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5M9	protein_coding	OTTHUMT00000391638.1	21	153	0	0.00	0	0	G	NM_001004743	0	0		56230566	-1	no_errors	ENST00000279791	ensembl	human	known	74_37	silent	10	102	44.44	42.46	8	76	SNP	0	A
CTSC	1075	genome.wustl.edu	37	11	88027335	88027335	+	Missense_Mutation	SNP	C	C	T	rs553675331		TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr11:88027335C>T	ENST00000227266.5	-	7	1345	c.1231G>A	c.(1231-1233)Ggc>Agc	p.G411S		NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	411					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GTGCCATAGCCCACAAGCAGA	0.517																																							0											0													134.0	108.0	117.0					11																	88027335		2201	4299	6500	SO:0001583	missense	0			AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.1231G>A	11.37:g.88027335C>T	ENSP00000227266:p.Gly411Ser		A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Missense_Mutation	SNP	pfam_Peptidase_C1A_C,pfam_CathepsinC_exc,smart_Peptidase_C1A_C,prints_Peptidase_C1A_C	p.G411S	ENST00000227266.5	37	c.1231	CCDS8282.1	11	.	.	.	.	.	.	.	.	.	.	C	25.3	4.628215	0.87560	.	.	ENSG00000109861	ENST00000393302;ENST00000227266	D	0.99338	-5.76	5.97	5.97	0.96955	Peptidase C1A, papain C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99736	0.9896	H	0.98333	4.205	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.83275	0.994;0.996	D	0.97326	0.9947	9	.	.	.	.	20.428	0.99075	0.0:1.0:0.0:0.0	.	394;411	B4DJQ8;P53634	.;CATC_HUMAN	S	394;411	ENSP00000227266:G411S	.	G	-	1	0	CTSC	87666983	1.000000	0.71417	0.997000	0.53966	0.320000	0.28249	7.786000	0.85741	2.837000	0.97791	0.655000	0.94253	GGC	0	pfam_Peptidase_C1A_C,smart_Peptidase_C1A_C,prints_Peptidase_C1A_C		0.517	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTSC	protein_coding	OTTHUMT00000394019.2	42	110	0	0.00	0	0	C	NM_001814	0	0		88027335	-1	no_errors	ENST00000227266	ensembl	human	known	74_37	missense	22	86	43.59	33.33	17	43	SNP	1	T
COL4A1	1282	genome.wustl.edu	37	13	110822103	110822103	+	Missense_Mutation	SNP	G	G	A			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr13:110822103G>A	ENST00000375820.4	-	43	3870	c.3749C>T	c.(3748-3750)cCg>cTg	p.P1250L		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	1250	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CATGGGTCCCGGAAGTCCTAA	0.572																																							0											0													60.0	68.0	65.0					13																	110822103		2203	4300	6503	SO:0001583	missense	0			J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.3749C>T	13.37:g.110822103G>A	ENSP00000364979:p.Pro1250Leu		A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.P1250L	ENST00000375820.4	37	c.3749	CCDS9511.1	13	.	.	.	.	.	.	.	.	.	.	G	23.4	4.413585	0.83449	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198	D	0.97731	-4.51	5.46	5.46	0.80206	.	0.188390	0.46145	D	0.000302	D	0.98498	0.9499	M	0.83384	2.64	0.80722	D	1	D	0.71674	0.998	P	0.58820	0.846	D	0.99267	1.0892	10	0.62326	D	0.03	.	18.3064	0.90184	0.0:0.0:1.0:0.0	.	1250	P02462	CO4A1_HUMAN	L	893;1250;899	ENSP00000364979:P1250L	ENSP00000364973:P893L	P	-	2	0	COL4A1	109620104	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.888000	0.69758	2.543000	0.85770	0.544000	0.68410	CCG	0	NULL		0.572	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A1	protein_coding	OTTHUMT00000045759.3	72	167	0	0.00	0	0	G		0	0		110822103	-1	no_errors	ENST00000375820	ensembl	human	known	74_37	missense	61	170	12.86	7.57	9	14	SNP	1	A
GYS1	2997	genome.wustl.edu	37	19	49477938	49477938	+	Missense_Mutation	SNP	T	T	C			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr19:49477938T>C	ENST00000323798.3	-	11	1557	c.1361A>G	c.(1360-1362)gAc>gGc	p.D454G	GYS1_ENST00000263276.6_Missense_Mutation_p.D390G|GYS1_ENST00000541188.1_Missense_Mutation_p.D374G|GYS1_ENST00000544287.1_Missense_Mutation_p.D87G|GYS1_ENST00000540532.1_3'UTR	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	454					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		CAGGATGGGGTCTGAGGAGTC	0.592																																							0											0													76.0	66.0	69.0					19																	49477938		2203	4300	6503	SO:0001583	missense	0				CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.1361A>G	19.37:g.49477938T>C	ENSP00000317904:p.Asp454Gly		Q9BTT9	Missense_Mutation	SNP	pfam_Glycogen_synth,pfam_Glyco_trans_1,pfam_Starch_synth_cat_dom	p.D454G	ENST00000323798.3	37	c.1361	CCDS12747.1	19	.	.	.	.	.	.	.	.	.	.	T	26.1	4.708685	0.89018	.	.	ENSG00000104812	ENST00000323798;ENST00000263276;ENST00000541188;ENST00000544287	T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.89051	0.6605	H	0.94183	3.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.91575	0.5274	10	0.87932	D	0	-39.0638	12.3811	0.55307	0.0:0.0:0.0:1.0	.	374;390;454	B7Z806;Q9BTT9;P13807	.;.;GYS1_HUMAN	G	454;390;374;87	ENSP00000317904:D454G;ENSP00000263276:D390G;ENSP00000437922:D374G;ENSP00000444004:D87G	ENSP00000263276:D390G	D	-	2	0	GYS1	54169750	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.789000	0.85783	1.972000	0.57404	0.459000	0.35465	GAC	0	pfam_Glycogen_synth		0.592	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GYS1	protein_coding	OTTHUMT00000319791.1	54	81	0	0.00	0	0	T	NM_002103	0	0		49477938	-1	no_errors	ENST00000323798	ensembl	human	known	74_37	missense	38	62	20.83	30.34	10	27	SNP	1	C
PLXNB2	23654	genome.wustl.edu	37	22	50721178	50721178	+	Silent	SNP	G	G	C			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr22:50721178G>C	ENST00000449103.1	-	18	3089	c.2949C>G	c.(2947-2949)ccC>ccG	p.P983P	PLXNB2_ENST00000359337.4_Silent_p.P983P|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	983	IPT/TIG 3.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CTCGCAGTACGGGGTTTTCGC	0.682																																							0											0													23.0	30.0	28.0					22																	50721178		1945	4112	6057	SO:0001819	synonymous_variant	0				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2949C>G	22.37:g.50721178G>C			A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_IPT,pfam_Semap_dom,pfam_Plexin_repeat,superfamily_Semap_dom,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semap_dom,smart_Plexin-like_fold,smart_IPT,pfscan_Semap_dom	p.P983	ENST00000449103.1	37	c.2949	CCDS43035.1	22																																																																																			0	pfam_IPT,superfamily_Ig_E-set,smart_IPT		0.682	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXNB2	protein_coding	OTTHUMT00000316874.3	169	117	0	0.00	0	0	G	NM_012401	0	0		50721178	-1	no_errors	ENST00000359337	ensembl	human	known	74_37	silent	78	75	37.6	38.02	47	46	SNP	0	C
MTMR8	55613	genome.wustl.edu	37	X	63488791	63488806	+	Frame_Shift_Del	DEL	TATTCAGGTCTCCATT	TATTCAGGTCTCCATT	-	rs144545484	byFrequency	TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	TATTCAGGTCTCCATT	TATTCAGGTCTCCATT	TATTCAGGTCTCCATT	-	TATTCAGGTCTCCATT	TATTCAGGTCTCCATT	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chrX:63488791_63488806delTATTCAGGTCTCCATT	ENST00000374852.3	-	14	1793_1808	c.1726_1741delAATGGAGACCTGAATA	c.(1726-1743)aatggagacctgaataccfs	p.NGDLNT576fs	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	576						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)|p.T581A(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TCCATCAGGGTATTCAGGTCTCCATTGATACCCATA	0.486																																							0											3	Whole gene deletion(2)|Substitution - Missense(1)	large_intestine(2)|ovary(1)																																								SO:0001589	frameshift_variant	0			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1726_1741delAATGGAGACCTGAATA	X.37:g.63488791_63488806delTATTCAGGTCTCCATT	ENSP00000363985:p.Asn576fs		Q5JT99|Q9NXP6	Frame_Shift_Del	DEL	pfam_Myotubularin-like_Pase_dom,smart_Tyr_Pase_cat	p.N576fs	ENST00000374852.3	37	c.1741_1726	CCDS14379.1	X																																																																																			0	NULL		0.486	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTMR8	protein_coding	OTTHUMT00000056949.2	31	96	0	0.00	0	0	TATTCAGGTCTCCATT	NM_017677	0	0		63488806	-1	no_errors	ENST00000374852	ensembl	human	known	74_37	frame_shift_del	1	27	80	35.71	4	15	DEL	0.954:0.927:0.899:0.866:0.739:0.694:0.647:0.629:0.633:0.635:0.631:0.598:0.416:0.136:0.046:0.015	0
HMX3	340784	genome.wustl.edu	37	10	124895626	124895627	+	Frame_Shift_Ins	INS	-	-	C			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr10:124895626_124895627insC	ENST00000357878.5	+	1	149_150	c.60_61insC	c.(61-63)cccfs	p.P21fs		NM_001105574.1	NP_001099044.1	A6NHT5	HMX3_HUMAN	H6 family homeobox 3	21	Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|embryo implantation (GO:0007566)|inner ear morphogenesis (GO:0042472)|maternal process involved in female pregnancy (GO:0060135)|neuromuscular process controlling balance (GO:0050885)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			lung(4)	4		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.122)|COAD - Colon adenocarcinoma(40;0.141)		AACCGCCGCCGCCCCCCCCACC	0.748																																							0											0																																										SO:0001589	frameshift_variant	0				CCDS41575.1	10q26.13	2011-06-20	2007-07-09		ENSG00000188620	ENSG00000188620		"""Homeoboxes / ANTP class : NKL subclass"""	5019	protein-coding gene	gene with protein product		613380	"""homeo box (H6 family) 3"""				Standard	NM_001105574		Approved	NKX5-1	uc010quc.2	A6NHT5	OTTHUMG00000019199	ENST00000357878.5:c.68dupC	10.37:g.124895634_124895634dupC	ENSP00000350549:p.Pro21fs		A8MU06	Frame_Shift_Ins	INS	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom,prints_Homeobox_metazoa	p.P23fs	ENST00000357878.5	37	c.60_61	CCDS41575.1	10																																																																																			0	NULL		0.748	HMX3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	HMX3	protein_coding	OTTHUMT00000050842.4	17	27	0	0.00	0	0	0	XM_291716	0	0		124895627	1	no_errors	ENST00000357878	ensembl	human	known	74_37	frame_shift_ins	6	42	45.45	14.29	5	7	INS	0.958:0.997	C
WASH6P	653440	genome.wustl.edu	37	X	155252253	155252253	+	RNA	SNP	C	C	T			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chrX:155252253C>T	ENST00000461007.1	+	0	1261				AJ271736.10_ENST00000285718.7_RNA			Q9NQA3	WASH6_HUMAN	WAS protein family homolog 6 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										TGGCTCGGCTCGGGAGGCCTG	0.672																																							0											0																																												0			AI042587		Xq28 and Yq12	2014-08-28	2008-01-16	2008-01-16	ENSG00000182484	ENSG00000182484		"""Pseudoautosomal regions / PAR2"", ""WAS protein homologs"""	31685	pseudogene	pseudogene			"""family with sequence similarity 39, member A"", ""chromosomes X and Y open reading frame 1"""	FAM39A, CXYorf1		10655549, 12566406, 18159949	Standard	NG_008380		Approved			Q9NQA3	OTTHUMG00000022677		X.37:g.155252253C>T			A6NGF1|Q8N305	RNA	SNP	0	NULL	ENST00000461007.1	37	NULL		X																																																																																			0	0		0.672	WASH6P-016	KNOWN	basic	processed_transcript	WASH6P	pseudogene	OTTHUMT00000058840.1	54	0	1.82	0.00	1	0	C	NG_008380	0	0		155252253	1	no_errors	ENST00000340131	ensembl	human	known	74_37	rna	43	0	15.69	0.00	8	0	SNP	0.77	T
KRT8P47	644743	genome.wustl.edu	37	1	44569970	44569970	+	lincRNA	SNP	A	A	C	rs71587039		TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr1:44569970A>C	ENST00000434244.1	+	0	1967																											CTCCAGCTTCAGCTTCTCCTG	0.547																																							0											0																																												0																															1.37:g.44569970A>C				RNA	SNP	0	NULL	ENST00000434244.1	37	NULL		1																																																																																			0	0		0.547	RP5-1198O20.4-001	KNOWN	basic	lincRNA	ENSG00000230615	lincRNA	OTTHUMT00000022875.2	19	0	0	0.00	0	0	A		0	0		44569970	1	no_errors	ENST00000434244	ensembl	human	known	74_37	rna	22	0	21.43	0.00	6	0	SNP	1	C
DNM1P47	100216544	genome.wustl.edu	37	15	102304649	102304649	+	RNA	SNP	G	G	T			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr15:102304649G>T	ENST00000561463.1	+	0	12695									DNM1 pseudogene 47																		ACTTGTGGAGGGGTCGGCAGA	0.607																																							0											0																																												0			AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102304649G>T				RNA	SNP	0	NULL	ENST00000561463.1	37	NULL		15																																																																																			0	0		0.607	DNM1P47-001	KNOWN	basic	processed_transcript	DNM1P47	pseudogene	OTTHUMT00000417589.1	10	0	0	0.00	0	0	G	NG_009149	0	0		102304649	1	no_errors	ENST00000561463	ensembl	human	known	74_37	rna	10	0	23.08	0.00	3	0	SNP	1	T
FAM230A	653203	genome.wustl.edu	37	22	20710913	20710913	+	Missense_Mutation	SNP	G	G	A	rs62218188		TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chr22:20710913G>A	ENST00000434783.3	+	8	2829	c.2645G>A	c.(2644-2646)aGg>aAg	p.R882K	USP41_ENST00000454608.2_Intron|USP41_ENST00000486536.2_Intron					family with sequence similarity 230, member A																		TCGCTAACGAGGACGCCGCCC	0.677																																							0											0																																										SO:0001583	missense	0			JX456222		22q11.21	2014-08-13			ENSG00000188280	ENSG00000188280			45045	other	unknown							Standard	XM_006724099		Approved	DGCR15			OTTHUMG00000150686	ENST00000434783.3:c.2645G>A	22.37:g.20710913G>A	ENSP00000463576:p.Arg882Lys			Missense_Mutation	SNP	pfam_Ret-finger_pr-like_3_antisense,superfamily_Kinase-like_dom	p.R882K	ENST00000434783.3	37	c.2645		22																																																																																			0	NULL		0.677	FAM230A-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	FAM230A	protein_coding	OTTHUMT00000319609.4	53	0	1.85	0.00	1	0	G		rs62218188	G->A		20710913	1	no_errors	ENST00000434783	ensembl	human	known	74_37	missense	62	3	11.43	0.00	8	0	SNP	0.158	A
CTAG2	30848	genome.wustl.edu	37	X	153881625	153881625	+	Frame_Shift_Del	DEL	C	C	-			TCGA-XM-AAZ2-01A-11D-A423-09	TCGA-XM-AAZ2-12A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3c2d3ad3-94dd-44c5-8194-db4fd3d95d92	ddc16e80-95c0-4d7c-b180-cd34e2927be4	g.chrX:153881625delC	ENST00000247306.4	-	1	228	c.165delG	c.(163-165)gggfs	p.G55fs	CTAG2_ENST00000369585.3_Frame_Shift_Del_p.G55fs	NM_020994.3	NP_066274.2	O75638	CTAG2_HUMAN	cancer/testis antigen 2	55	Gly-rich.					centrosome (GO:0005813)				central_nervous_system(1)|endometrium(1)|lung(6)|ovary(1)|pancreas(1)	10	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTCCTCTCGGCCCCGAGGCCC	0.761																																							0											0													10.0	12.0	11.0					X																	153881625		2073	4036	6109	SO:0001589	frameshift_variant	0			AJ012833	CCDS14759.1, CCDS35455.1	Xq28	2009-08-18			ENSG00000126890	ENSG00000126890			2492	protein-coding gene	gene with protein product	"""CTL-recognized antigen on melanoma"", ""LAGE-1a protein"", ""cancer/testis antigen family 6, member 2a"", ""cancer/testis antigen family 6, member 2b"""	300396				9626360, 10399963	Standard	NM_020994		Approved	LAGE-1, CAMEL, LAGE1, ESO2, MGC3803, MGC138724, CT6.2a, CT6.2b, LAGE-1a, LAGE-1b	uc004fmi.2	O75638	OTTHUMG00000024239	ENST00000247306.4:c.165delG	X.37:g.153881625delC	ENSP00000247306:p.Gly55fs		O75637|Q0VIL6|Q14CD6|Q2Z1N4|Q9BU80|Q9UJ89|Q9Y479	Frame_Shift_Del	DEL	pfam_EKC/KEOPS_Pcc1	p.P56fs	ENST00000247306.4	37	c.165	CCDS14759.1	X																																																																																			0	NULL		0.761	CTAG2-001	PUTATIVE	basic|CCDS	protein_coding	CTAG2	protein_coding	OTTHUMT00000061176.1	9	0	0	0.00	0	0	C	NM_020994	0	0		153881625	-1	no_errors	ENST00000369585	ensembl	human	known	74_37	frame_shift_del	4	2	33.33	0.00	2	0	DEL	0	0
