#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_ENSG_ID	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_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	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_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	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_reference	i_refseq_mrna_id	i_rs_id	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_type	i_ucsc_cons	i_variant
PRR4	11272	genome.wustl.edu	37	12	11035107	11035107	+	Intron	SNP	T	T	C	rs2946841		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr12:11035107T>C	ENST00000536668.1	-	8	822				PRH1_ENST00000428168.2_Intron	NR_037918.1		Q16378	PROL4_HUMAN	proline rich 4 (lacrimal)						retina homeostasis (GO:0001895)|visual perception (GO:0007601)	extracellular space (GO:0005615)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	9						GCTGGCCTCCTTGTTGGGGTG	0.617																																																	0								ENSG00000111215						150.0	55.0	91.0					12																	11035107		2040	3331	5371	PRR4	SO:0001627	intron_variant	0			-	HGNC		CCDS41756.1, CCDS55804.1	12p13	2008-02-05		2004-05-28		ENSG00000111215			18020	protein-coding gene	gene with protein product		605359		PROL4		7544782	Standard	NM_007244		Approved	LPRP	uc001qyz.4	Q16378		ENST00000536668.1:c.734-20A>G	12.37:g.11035107T>C		Somatic	0	13	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	7	41.67	A8KA69|F5H0D7|Q8NFB3	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000536668.1	37	NULL		12																																																																																			-	-		0.617	PRR4-002	KNOWN	basic	processed_transcript	PRR4	protein_coding	OTTHUMT00000400050.2	T	NM_007244	rs2946841		11035107	-1	no_errors	ENST00000543626	ensembl	human	known	74_37	rna	SNP	0.001	C
CGN	57530	genome.wustl.edu	37	1	151503079	151503079	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:151503079G>T	ENST00000271636.7	+	13	2561	c.2428G>T	c.(2428-2430)Gcc>Tcc	p.A810S	SNORA44_ENST00000517031.1_RNA	NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	804	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCGGGGGCTGGCCCGCCTGGG	0.697																																																	0								ENSG00000143375						16.0	18.0	17.0					1																	151503079		2197	4290	6487	CGN	SO:0001583	missense	0			-	HGNC	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.2428G>T	1.37:g.151503079G>T	ENSP00000271636:p.Ala810Ser	Somatic	0	35	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	22	15.38	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Myosin_tail	p.A810S	ENST00000271636.7	37	c.2428	CCDS999.1	1	.	.	.	.	.	.	.	.	.	.	G	2.292	-0.362207	0.05103	.	.	ENSG00000143375	ENST00000271636	T	0.62639	0.01	4.99	-1.44	0.08856	.	0.484241	0.24659	N	0.036643	T	0.09423	0.0232	N	0.03608	-0.345	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.37056	-0.9722	10	0.07813	T	0.8	-0.0757	5.3336	0.15945	0.4638:0.0:0.4026:0.1336	.	804	Q9P2M7	CING_HUMAN	S	810	ENSP00000271636:A810S	ENSP00000271636:A810S	A	+	1	0	CGN	149769703	0.002000	0.14202	0.875000	0.34327	0.967000	0.64934	-0.052000	0.11865	-0.175000	0.10725	-0.259000	0.10710	GCC	-	NULL		0.697	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CGN	protein_coding	OTTHUMT00000034900.3	G	NM_020770	-		151503079	+1	no_errors	ENST00000271636	ensembl	human	known	74_37	missense	SNP	0.001	T
OR11G2	390439	genome.wustl.edu	37	14	20666175	20666176	+	Frame_Shift_Ins	INS	-	-	A	rs398102302|rs200876108|rs77164062|rs55781225|rs398077614	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr14:20666175_20666176insA	ENST00000357366.3	+	1	681_682	c.681_682insA	c.(682-684)aaafs	p.K228fs		NM_001005503.1	NP_001005503.1	Q8NGC1	O11G2_HUMAN	olfactory receptor, family 11, subfamily G, member 2	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G230fs*74(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(95;0.00108)		Epithelial(56;9.76e-07)|all cancers(55;5.61e-06)	GBM - Glioblastoma multiforme(265;0.0144)		CTCTCACTTGCAAAAAAGGCCC	0.45																																																	1	Insertion - Frameshift(1)	ovary(1)						ENSG00000196832			2850,1414		945,960,227						3.1	0.6		dbSNP_130	125	5846,2408		2086,1674,367	no	frameshift	OR11G2	NM_001005503.1		3031,2634,594	A1A1,A1R,RR		29.1737,33.1614,30.532				8696,3822				OR11G2	SO:0001589	frameshift_variant	0				HGNC		CCDS32032.1	14q11.2	2013-09-24			ENSG00000196832	ENSG00000196832		"""GPCR / Class A : Olfactory receptors"""	15346	protein-coding gene	gene with protein product							Standard	NM_001005503		Approved		uc010tlb.2	Q8NGC1	OTTHUMG00000167700	ENST00000357366.3:c.687dupA	14.37:g.20666181_20666181dupA	ENSP00000349930:p.Lys228fs	Somatic	0	71	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	86	8.51	Q6IF09|Q96R33	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.G229fs	ENST00000357366.3	37	c.681_682	CCDS32032.1	14																																																																																			-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt		0.450	OR11G2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	OR11G2	protein_coding	OTTHUMT00000395722.1	-				20666176	+1	no_errors	ENST00000357366	ensembl	human	known	74_37	frame_shift_ins	INS	0.830:0.001	A
SLC23A2	9962	genome.wustl.edu	37	20	4850569	4850569	+	Frame_Shift_Del	DEL	G	G	-			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr20:4850569delG	ENST00000379333.1	-	12	1625	c.1233delC	c.(1231-1233)cccfs	p.P411fs	SLC23A2_ENST00000338244.1_Frame_Shift_Del_p.P411fs|SLC23A2_ENST00000424750.2_Frame_Shift_Del_p.P297fs|SNORA31_ENST00000516287.1_RNA|SLC23A2_ENST00000468355.1_5'UTR	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	411					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.I412fs*4(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TTGCGTGGATGGGGGGGGGTG	0.527																																																	1	Deletion - Frameshift(1)	ovary(1)						ENSG00000089057						65.0	70.0	68.0					20																	4850569		2203	4300	6503	SLC23A2	SO:0001589	frameshift_variant	0				HGNC	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.1233delC	20.37:g.4850569delG	ENSP00000368637:p.Pro411fs	Somatic	0	31	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	29	19.44	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Xant/urac/vitC	p.I412fs	ENST00000379333.1	37	c.1233	CCDS13085.1	20																																																																																			-	pfam_Xant/urac/vitC		0.527	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC23A2	protein_coding	OTTHUMT00000077832.1	G				4850569	-1	no_errors	ENST00000338244	ensembl	human	known	74_37	frame_shift_del	DEL	0.974	-
AOX2P	344454	genome.wustl.edu	37	2	201619757	201619758	+	IGR	INS	-	-	TG	rs71022335|rs35856862|rs563268698	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr2:201619757_201619758insTG								AC007163.3 (19857 upstream) : AOX2P (7272 downstream)																							TCCTTTCAAATtgtgtgtgtgt	0.401																																																	0								ENSG00000243478																																			AOX2P	SO:0001628	intergenic_variant	0				HGNC																													2.37:g.201619766_201619767dupTG		Somatic	0	11	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	15	31.82		RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL		37	NULL		2																																																																																			-	-	0	0.401					AOX2P			-				201619758	+1	no_errors	ENST00000472376	ensembl	human	known	74_37	rna	INS	0.000:0.000	TG
MT-ND5	4540	genome.wustl.edu	37	M	12684	12684	+	Silent	SNP	G	G	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:12684G>A	ENST00000361567.2	+	1	348	c.348G>A	c.(346-348)caG>caA	p.Q116Q	MT-TH_ENST00000387441.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	116					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AACATTAATCAGTTCTTCAAA	0.368																																																	0								ENSG00000198786																																			MT-ND5	SO:0001819	synonymous_variant	0			-	HGNC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.348G>A	M.37:g.12684G>A		Somatic	0	188	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	25	19.35	Q34773|Q8WCY3	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_NADH_UbQ/plastoQ_OxRdtase,pfam_NADH_DH_su5_C,pfam_NADH_UbQ_OxRdtase_chain5/L_N,tigrfam_NADHpl_OxRdtase_5	p.Q116	ENST00000361567.2	37	c.348		MT																																																																																			-	pfam_NADH_UbQ_OxRdtase_chain5/L_N,tigrfam_NADHpl_OxRdtase_5		0.368	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	protein_coding		G	YP_003024036	rs28410409		12684	+1	no_errors	ENST00000361567	ensembl	human	known	74_37	silent	SNP	NULL	A
MYO5B	4645	genome.wustl.edu	37	18	47363917	47363917	+	Missense_Mutation	SNP	A	A	G	rs138128932	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr18:47363917A>G	ENST00000285039.7	-	37	5407	c.5108T>C	c.(5107-5109)gTc>gCc	p.V1703A	MYO5B_ENST00000592688.1_Missense_Mutation_p.V273A|SCARNA17_ENST00000589499.1_RNA|MYO5B_ENST00000324581.6_Missense_Mutation_p.V818A|RP11-886H22.1_ENST00000590532.2_Missense_Mutation_p.V26A	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1703	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.V1703A(5)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		CCAAGAGCAGACGTCCTTCCG	0.527																																																	5	Substitution - Missense(5)	endometrium(2)|kidney(2)|lung(1)						ENSG00000167306						70.0	68.0	69.0					18																	47363917		2027	4186	6213	MYO5B	SO:0001583	missense	0			-	HGNC	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.5108T>C	18.37:g.47363917A>G	ENSP00000285039:p.Val1703Ala	Somatic	0	77	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	70	10.26	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Myosin_head_motor_dom,pfam_Dil_domain,pfam_IQ_motif_EF-hand-BS,superfamily_P-loop_NTPase,superfamily_Prefoldin,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,pfscan_Dilute,pfscan_IQ_motif_EF-hand-BS,prints_Myosin_head_motor_dom	p.V1703A	ENST00000285039.7	37	c.5108	CCDS42436.1	18	.	.	.	.	.	.	.	.	.	.	A	14.46	2.542024	0.45280	.	.	ENSG00000167306	ENST00000285039;ENST00000324581	D;T	0.86432	-2.12;2.51	4.77	0.996	0.19844	Dilute (1);Dil domain (1);	0.146358	0.45126	N	0.000396	T	0.78534	0.4298	L	0.40543	1.245	0.36910	D	0.890859	B;B	0.13145	0.001;0.007	B;B	0.21708	0.012;0.036	T	0.66284	-0.5962	10	0.19147	T	0.46	.	8.6034	0.33758	0.7815:0.0:0.2185:0.0	.	1703;818	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	A	1703;818	ENSP00000285039:V1703A;ENSP00000315531:V818A	ENSP00000285039:V1703A	V	-	2	0	MYO5B	45617915	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.310000	0.59141	0.082000	0.17018	0.482000	0.46254	GTC	-	pfam_Dil_domain,pfscan_Dilute		0.527	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYO5B	protein_coding	OTTHUMT00000448515.2	A		rs138128932		47363917	-1	no_errors	ENST00000285039	ensembl	human	known	74_37	missense	SNP	1.000	G
CCDC66	285331	genome.wustl.edu	37	3	56650051	56650052	+	In_Frame_Ins	INS	-	-	CTT	rs67797937|rs77152637|rs74463118	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr3:56650051_56650052insCTT	ENST00000394672.3	+	13	1883_1884	c.1813_1814insCTT	c.(1813-1815)act>aCTTct	p.606_607insS	CCDC66_ENST00000326595.7_In_Frame_Ins_p.572_573insS|CCDC66_ENST00000436465.2_In_Frame_Ins_p.606_607insS	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	606					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		GAATTCTACGACTTCTAAGAAG	0.287																																																	0								ENSG00000180376		,	3586,680		1520,546,67					,	1.9	0.0		dbSNP_130	92	3788,4448		872,2044,1202	no	coding,coding	CCDC66	NM_001141947.1,NM_001012506.4	,	2392,2590,1269	A1A1,A1R,RR		45.9932,15.94,41.0174	,	,		7374,5128				CCDC66	SO:0001652	inframe_insertion	0				HGNC	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1814_1816dupCTT	3.37:g.56650052_56650054dupCTT	ENSP00000378167:p.Ser606_Ser606dup	Somatic	0	20	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	25	10.71	B3KWL8|Q4VC34|Q8N949	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	NULL	p.607in_frame_insS	ENST00000394672.3	37	c.1813_1814	CCDS46852.1	3																																																																																			-	NULL		0.287	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CCDC66	protein_coding	OTTHUMT00000341473.1	-	NM_001012506			56650052	+1	no_errors	ENST00000394672	ensembl	human	known	74_37	in_frame_ins	INS	0.002:0.009	CTT
NOP56	10528	genome.wustl.edu	37	20	2633378	2633379	+	Intron	INS	-	-	GAGCCTGGGCCT	rs71328095|rs149713688	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr20:2633378_2633379insGAGCCTGGGCCT	ENST00000329276.5	+	1	519				MIR1292_ENST00000408135.1_RNA|SNORA51_ENST00000606420.1_RNA|SNORD110_ENST00000408189.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein						cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GGCCGCAGACAgggcctgggcc	0.748														1743	0.348043	0.2655	0.3329	5008	,	,		12117	0.4038		0.325	False		,,,				2504	0.4366																0								ENSG00000101361			2444,1274		918,608,333						-1.2	0.0		dbSNP_134	7	4565,2715		1533,1499,608	no	intron	NOP56	NM_006392.3		2451,2107,941	A1A1,A1R,RR		37.294,34.2657,36.2702				7009,3989				NOP56	SO:0001627	intron_variant	0				HGNC	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.3+69->GAGCCTGGGCCT	20.37:g.2633378_2633379insGAGCCTGGGCCT		Somatic	NA	NA	NA		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q2M3T6|Q9NQ05	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000329276.5	37	NULL	CCDS13030.1	20																																																																																			-	-		0.748	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NOP56	protein_coding	OTTHUMT00000077631.2	-	NM_006392			2633379	+1	no_errors	ENST00000469588	ensembl	human	known	74_37	rna	INS	0.000:0.000	GAGCCTGGGCCT
GLIPR1L2	144321	genome.wustl.edu	37	12	75816814	75816815	+	Intron	INS	-	-	ACA	rs199738162|rs397750292|rs144850646|rs59277111	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr12:75816814_75816815insACA	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000320460.4_In_Frame_Ins_p.239_240insN|GLIPR1L2_ENST00000441218.1_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TAATGGATTGGACAAGAAAAAT	0.312														1714	0.342252	0.2511	0.2622	5008	,	,		17045	0.4683		0.3767	False		,,,				2504	0.3569																0								ENSG00000180481			1181,3083		163,855,1114						0.0	0.0		dbSNP_130	117	3246,5006		650,1946,1530	no	coding	GLIPR1L2	NM_152436.1		813,2801,2644	A1A1,A1R,RR		39.3359,27.697,35.3707				4427,8089				GLIPR1L2	SO:0001627	intron_variant	0				HGNC	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+45->ACA	12.37:g.75816815_75816817dupACA		Somatic	0	28	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	22	8.33	Q6MZS1|Q8N6N0|Q8NA43	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_CAP_domain,superfamily_CAP_domain,smart_Allrgn_V5/Tpx1,prints_Allrgn_V5/Tpx1	p.240in_frame_insN	ENST00000550916.1	37	c.715_716	CCDS58258.1	12																																																																																			-	NULL		0.312	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GLIPR1L2	protein_coding	OTTHUMT00000405718.1	-	NM_152436			75816815	+1	no_errors	ENST00000320460	ensembl	human	known	74_37	in_frame_ins	INS	0.000:0.000	ACA
HRNR	388697	genome.wustl.edu	37	1	152188847	152188847	+	Missense_Mutation	SNP	A	A	G	rs145667921		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:152188847A>G	ENST00000368801.2	-	3	5333	c.5258T>C	c.(5257-5259)gTc>gCc	p.V1753A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1753					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGACCAAAGACAGAAGAGTG	0.562																																																	0								ENSG00000197915						1.0	1.0	1.0					1																	152188847		388	960	1348	HRNR	SO:0001583	missense	0			-	HGNC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5258T>C	1.37:g.152188847A>G	ENSP00000357791:p.Val1753Ala	Somatic	0	28	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	19	17.39	Q5DT20|Q5U1F4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_S100_Ca-bd_sub,pfscan_EF_hand_dom	p.V1753A	ENST00000368801.2	37	c.5258	CCDS30859.1	1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191978	0.38707	.	.	ENSG00000197915	ENST00000368801	T	0.01548	4.78	3.15	2.19	0.27852	.	.	.	.	.	T	0.00412	0.0013	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48103	-0.9064	9	0.07482	T	0.82	.	1.9459	0.03356	0.2121:0.4632:0.2061:0.1186	.	1753	Q86YZ3	HORN_HUMAN	A	1753	ENSP00000357791:V1753A	ENSP00000357791:V1753A	V	-	2	0	HRNR	150455471	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.214000	0.09292	0.170000	0.19704	-0.294000	0.09567	GTC	-	NULL		0.562	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HRNR	protein_coding	OTTHUMT00000034016.1	A	XM_373868	rs145667921		152188847	-1	no_errors	ENST00000368801	ensembl	human	known	74_37	missense	SNP	0.002	G
MT-CO1	4512	genome.wustl.edu	37	M	6733	6733	+	Missense_Mutation	SNP	T	T	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:6733T>A	ENST00000361624.2	+	1	830	c.830T>A	c.(829-831)aTg>aAg	p.M277K	MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TW_ENST00000387382.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	277					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						GGTCTGAGCTATGATATCAAT	0.393																																																	0								ENSG00000198804																																			MT-CO1	SO:0001583	missense	0			-	HGNC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.830T>A	M.37:g.6733T>A	ENSP00000354499:p.Met277Lys	Somatic	0	153	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	13	13.33	Q34770	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom,prints_Cyt_c_Oxase_su1	p.M277K	ENST00000361624.2	37	c.830		MT																																																																																			-	pfam_Cyt_c_Oxase_su1,superfamily_Cyt_c_Oxase_su1_dom,pfscan_Cyt_c_Oxase_su1_dom		0.393	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	MT-CO1	protein_coding		T	YP_003024028	-		6733	+1	no_errors	ENST00000361624	ensembl	human	known	74_37	missense	SNP	NULL	A
PPP2R2B	5521	genome.wustl.edu	37	5	146258290	146258291	+	5'UTR	INS	-	-	GCTGCTGCT	rs142461655|rs57408722|rs10591869	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr5:146258290_146258291insGCTGCTGCT	ENST00000453001.1	-	0	166_167				PPP2R2B_ENST00000394414.1_Intron|PPP2R2B_ENST00000508545.2_Intron|PPP2R2B_ENST00000394413.3_5'Flank|PPP2R2B_ENST00000394411.4_5'UTR|PPP2R2B_ENST00000336640.6_Intron|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000356826.3_Intron|PPP2R2B_ENST00000504198.1_Intron|PPP2R2B_ENST00000394410.2_Intron|PPP2R2B_ENST00000394409.3_Intron			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta						apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCGCACTCGCAgctgctgctgc	0.718														1222	0.24401	0.2375	0.2262	5008	,	,		13292	0.3562		0.1421	False		,,,				2504	0.2546																0								ENSG00000156475																																			PPP2R2B	SO:0001623	5_prime_UTR_variant	0				HGNC	M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9305	protein-coding gene	gene with protein product	"""PP2A subunit B isoform beta"""	604325	"""spinocerebellar ataxia 12"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"""	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000453001.1:c.-152->AGCAGCAGC	5.37:g.146258291_146258299dupGCTGCTGCT		Somatic	NA	NA	NA		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000453001.1	37	NULL	CCDS4284.1	5																																																																																			-	-		0.718	PPP2R2B-204	KNOWN	basic|appris_principal|CCDS	protein_coding	PPP2R2B	protein_coding	OTTHUMT00000388939.2	-	NM_181678			146258291	-1	no_errors	ENST00000530902	ensembl	human	known	74_37	rna	INS	0.975:0.996	GCTGCTGCT
AHDC1	27245	genome.wustl.edu	37	1	27878567	27878567	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:27878567G>T	ENST00000247087.5	-	5	656	c.60C>A	c.(58-60)gaC>gaA	p.D20E	AHDC1_ENST00000374011.2_Missense_Mutation_p.D20E			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	20							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		CCCGGAGGTAGTCAGGAGAGC	0.721																																																	0								ENSG00000126705						4.0	3.0	3.0					1																	27878567		1544	2808	4352	AHDC1	SO:0001583	missense	0			-	HGNC	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.60C>A	1.37:g.27878567G>T	ENSP00000247087:p.Asp20Glu	Somatic	0	26	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	11	21.43	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.D20E	ENST00000247087.5	37	c.60	CCDS30652.1	1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966755	0.53507	.	.	ENSG00000126705	ENST00000247087;ENST00000374011;ENST00000407475	T;T	0.53857	0.6;0.6	4.43	4.43	0.53597	.	0.000000	0.36740	U	0.002430	T	0.47875	0.1469	N	0.14661	0.345	0.28413	N	0.91807	D	0.55605	0.972	P	0.59948	0.866	T	0.37267	-0.9713	10	0.39692	T	0.17	-14.6329	8.4887	0.33086	0.1083:0.0:0.8917:0.0	.	20	Q5TGY3	AHDC1_HUMAN	E	20	ENSP00000247087:D20E;ENSP00000363123:D20E	ENSP00000247087:D20E	D	-	3	2	AHDC1	27751154	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.094000	0.57721	2.002000	0.58637	0.305000	0.20034	GAC	-	NULL		0.721	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AHDC1	protein_coding	OTTHUMT00000009523.3	G		-		27878567	-1	no_errors	ENST00000247087	ensembl	human	known	74_37	missense	SNP	1.000	T
ZNF578	147660	genome.wustl.edu	37	19	53015488	53015488	+	IGR	DEL	G	G	-	rs35772645	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr19:53015488delG	ENST00000421239.2	+	0	2017				CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		AAAAGACATAGGAGAATTCAT	0.418													GG|GG|G|deletion	828	0.165335	0.1558	0.2378	5008	,	,		23058	0.0437		0.2306	False		,,,				2504	0.1851																0								ENSG00000269349																																			CTD-3099C6.5	SO:0001628	intergenic_variant	0				Clone_based_vega_gene	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468		19.37:g.53015488delG		Somatic	0	43	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	36	10.00	B4DR51|I3L1Y6	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000421239.2	37	NULL	CCDS54310.1	19																																																																																			-	-		0.418	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	ENSG00000269349	protein_coding	OTTHUMT00000344298.3	G	NM_152472			53015488	-1	no_errors	ENST00000599143	ensembl	human	known	74_37	rna	DEL	0.001	-
ETV5	2119	genome.wustl.edu	37	3	185823280	185823280	+	Missense_Mutation	SNP	A	A	G			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr3:185823280A>G	ENST00000306376.5	-	4	385	c.139T>C	c.(139-141)Ttt>Ctt	p.F47L	DGKG_ENST00000447054.1_5'Flank|ETV5_ENST00000537818.1_Missense_Mutation_p.F89L|ETV5_ENST00000434744.1_Missense_Mutation_p.F47L	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	47					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|locomotory behavior (GO:0007626)|male germ-line stem cell asymmetric division (GO:0048133)|neuromuscular synaptic transmission (GO:0007274)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of synapse organization (GO:0050807)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	28	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			AGATCCTGAAATAGCTCTGAA	0.403			T	"""TMPRSS2, SCL45A3"""	Prostate																																			Dom	yes		3	3q28	2119	ets variant gene 5		E	0								ENSG00000244405						76.0	82.0	80.0					3																	185823280		2203	4300	6503	ETV5	SO:0001583	missense	0			-	HGNC	BC007333	CCDS33906.1	3q28	2008-09-12	2008-09-12		ENSG00000244405	ENSG00000244405			3494	protein-coding gene	gene with protein product	"""ets-related molecule"""	601600	"""ets variant gene 5 (ets-related molecule)"""			8152800	Standard	NM_004454		Approved	ERM	uc003fpz.3	P41161	OTTHUMG00000156639	ENST00000306376.5:c.139T>C	3.37:g.185823280A>G	ENSP00000306894:p.Phe47Leu	Somatic	0	36	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	39	22.00	A6NH46|B7Z7D7|Q6IBN5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_ETS_PEA3_N,pfam_Ets_dom,smart_Ets_dom,pfscan_Ets_dom,prints_Ets_dom	p.F89L	ENST00000306376.5	37	c.265	CCDS33906.1	3	.	.	.	.	.	.	.	.	.	.	A	22.7	4.328041	0.81690	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818;ENST00000440773;ENST00000421809;ENST00000413301;ENST00000422039	T;T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79;0.79	5.35	5.35	0.76521	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.052176	0.85682	D	0.000000	T	0.69133	0.3077	M	0.81112	2.525	0.51482	D	0.999927	D;D	0.69078	0.997;0.979	D;D	0.77004	0.989;0.982	T	0.73994	-0.3807	10	0.87932	D	0	.	13.1469	0.59467	1.0:0.0:0.0:0.0	.	47;89	P41161;B7Z7D7	ETV5_HUMAN;.	L	47;47;89;47;47;47;47	ENSP00000306894:F47L;ENSP00000413755:F47L;ENSP00000441737:F89L;ENSP00000389707:F47L;ENSP00000412171:F47L;ENSP00000405157:F47L;ENSP00000388737:F47L	ENSP00000306894:F47L	F	-	1	0	ETV5	187305974	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	8.226000	0.89785	2.147000	0.66899	0.379000	0.24179	TTT	-	pfam_ETS_PEA3_N		0.403	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ETV5	protein_coding	OTTHUMT00000344947.1	A	NM_004454	-		185823280	-1	no_errors	ENST00000537818	ensembl	human	known	74_37	missense	SNP	1.000	G
HYDIN	54768	genome.wustl.edu	37	16	70841824	70841824	+	Missense_Mutation	SNP	C	C	T	rs199657414		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr16:70841824C>T	ENST00000393567.2	-	86	15175	c.15025G>A	c.(15025-15027)Gca>Aca	p.A5009T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	5009					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TCTCCACCTGCGAGCGATGAT	0.582																																																	0								ENSG00000157423						87.0	91.0	90.0					16																	70841824		2000	4170	6170	HYDIN	SO:0001583	missense	0			-	HGNC	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.15025G>A	16.37:g.70841824C>T	ENSP00000377197:p.Ala5009Thr	Somatic	0	42	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	68	13.92	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	superfamily_P-loop_NTPase,superfamily_PapD-like	p.A5009T	ENST00000393567.2	37	c.15025	CCDS59269.1	16	.	.	.	.	.	.	.	.	.	.	C	3.757	-0.050399	0.07407	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00792	5.69	6.17	-7.19	0.01500	.	1.715750	0.04730	N	0.420971	T	0.00412	0.0013	N	0.04090	-0.28	0.09310	N	1	B	0.21688	0.059	B	0.15870	0.014	T	0.48352	-0.9043	10	0.14252	T	0.57	.	4.1725	0.10336	0.1094:0.4365:0.1801:0.274	.	5008	F8WD23	.	T	5009;5008	ENSP00000377197:A5009T	ENSP00000313052:A5008T	A	-	1	0	HYDIN	69399325	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.186000	0.03070	-1.845000	0.01176	-0.140000	0.14226	GCA	-	NULL		0.582	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	HYDIN	protein_coding	OTTHUMT00000398624.3	C		rs199657414		70841824	-1	no_errors	ENST00000393567	ensembl	human	putative	74_37	missense	SNP	0.000	T
MYB	4602	genome.wustl.edu	37	6	135518225	135518225	+	Intron	SNP	G	G	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr6:135518225G>A	ENST00000367814.4	+	9	1389				MYB_ENST00000533624.1_Intron|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000534044.1_Intron|MYB_ENST00000525369.1_Intron|MYB_ENST00000341911.5_Missense_Mutation_p.A444T|MYB_ENST00000534121.1_Missense_Mutation_p.A428T|MYB_ENST00000531845.1_Intron|MYB_ENST00000527615.1_Intron|MYB_ENST00000442647.2_Intron|MYB_ENST00000528774.1_Missense_Mutation_p.A441T|MYB_ENST00000316528.8_Intron	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		GACTAAACCTGCAGGAGAACC	0.478			T	NFIB	adenoid cystic carcinoma																																			Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	0								ENSG00000118513						159.0	143.0	148.0					6																	135518225		1568	3582	5150	MYB	SO:0001627	intron_variant	0			-	HGNC		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1203+1085G>A	6.37:g.135518225G>A		Somatic	0	38	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	36	10.00	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_C-myb_C,pfam_SANT/Myb,pfam_Tscrpt_reg_Wos2-domain,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom	p.A444T	ENST00000367814.4	37	c.1330	CCDS5174.1	6	.	.	.	.	.	.	.	.	.	.	G	0.233	-1.019168	0.02078	.	.	ENSG00000118513	ENST00000341911;ENST00000528774;ENST00000534121	T;T;T	0.12361	2.69;2.69;2.7	5.71	4.84	0.62591	.	0.790656	0.11915	N	0.517274	T	0.02807	0.0084	N	0.19112	0.55	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.0;0.001;0.003	T	0.37361	-0.9709	10	0.14252	T	0.57	-2.3337	7.7431	0.28853	0.1466:0.1448:0.7086:0.0	.	441;428;444	E9PNL6;E9PNA4;P10242-4	.;.;.	T	444;441;428	ENSP00000339992:A444T;ENSP00000434723:A441T;ENSP00000432851:A428T	ENSP00000339992:A444T	A	+	1	0	MYB	135559918	1.000000	0.71417	0.994000	0.49952	0.112000	0.19704	2.339000	0.43965	1.431000	0.47355	0.655000	0.94253	GCA	-	NULL		0.478	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MYB	protein_coding	OTTHUMT00000042347.4	G		-		135518225	+1	no_errors	ENST00000341911	ensembl	human	known	74_37	missense	SNP	0.965	A
TRPA1	8989	genome.wustl.edu	37	8	72935420	72935458	+	Intron	DEL	GCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAAC	GCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAAC	-	rs34076632|rs142191870|rs10089294	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	GCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAAC	GCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr8:72935420_72935458delGCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAAC	ENST00000262209.4	-	27	3357				RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1						calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATGTAGGAAGGCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAACGCATAGGTTT	0.372														2411	0.48143	0.4629	0.3617	5008	,	,		25826	0.7579		0.4384	False		,,,				2504	0.3507																0								ENSG00000104321																																			TRPA1	SO:0001627	intron_variant	0				HGNC	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.3150-69GTTCCTACATTCAGAAGGGACCGAGGTTAAAACCTATGC>-	8.37:g.72935420_72935458delGCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAAC		Somatic	NA	NA	NA		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A6NIN6	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000262209.4	37	NULL	CCDS34908.1	8																																																																																			-	-		0.372	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TRPA1	protein_coding	OTTHUMT00000379079.2	GCATAGGTTTTAACCTCGGTCCCTTCTGAATGTAGGAAC	NM_007332			72935458	-1	no_errors	ENST00000520596	ensembl	human	putative	74_37	rna	DEL	0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.001:0.001:0.001:0.001:0.000:0.000:0.000:0.000:0.000:0.002:0.002:0.000:0.000:0.000:0.000:0.000:0.001:0.002:0.001:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000	-
SCG3	29106	genome.wustl.edu	37	15	51987959	51987960	+	Intron	INS	-	-	A	rs78233272|rs370571693		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr15:51987959_51987960insA	ENST00000220478.3	+	8	1271				RP11-313P18.2_ENST00000559918.1_lincRNA|SCG3_ENST00000542355.2_Intron	NM_013243.3	NP_037375.2	Q8WXD2	SCG3_HUMAN	secretogranin III						blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				all cancers(107;0.00488)		cctcgtctttgaaaaaaaaaaa	0.401																																																	0								ENSG00000259241																																			RP11-313P18.2	SO:0001627	intron_variant	0				Clone_based_vega_gene	AF078851	CCDS10142.1, CCDS53947.1	15q21.2	2013-09-23			ENSG00000104112	ENSG00000104112			13707	protein-coding gene	gene with protein product		611796				2053134, 8825061	Standard	NM_013243		Approved	SGIII, FLJ90833	uc002abh.3	Q8WXD2	OTTHUMG00000131748	ENST00000220478.3:c.869-112->A	15.37:g.51987970_51987970dupA		Somatic	0	15	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	14	22.22	A8K2B0|B3KQP6|B4DK99|F5H3R8|Q96C83|Q96GE8|Q9Y6G7	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000220478.3	37	NULL	CCDS10142.1	15																																																																																			-	-		0.401	SCG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000259241	protein_coding	OTTHUMT00000254670.2	-	NM_013243			51987960	-1	no_errors	ENST00000559918	ensembl	human	known	74_37	rna	INS	0.003:0.006	A
MPC2	25874	genome.wustl.edu	37	1	167893759	167893759	+	Silent	SNP	G	G	A	rs9618	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:167893759G>A	ENST00000367846.4	-	2	324	c.126C>T	c.(124-126)ttC>ttT	p.F42F	MPC2_ENST00000271373.4_Silent_p.F42F	NM_015415.3	NP_056230.1	O95563	MPC2_HUMAN	mitochondrial pyruvate carrier 2	42					cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate transmembrane transporter activity (GO:0050833)										GAGCCCAGAAGAAAACTGTTC	0.299													A|||	2036	0.40655	0.6823	0.5202	5008	,	,		16494	0.1806		0.3519	False		,,,				2504	0.2423																0								ENSG00000143158	A	,	2624,1772		794,1036,368	17.0	19.0	18.0		126,126	2.1	1.0	1	dbSNP_79	18	2851,5725		507,1837,1944	no	coding-synonymous,coding-synonymous	BRP44	NM_001143674.2,NM_015415.3	,	1301,2873,2312	AA,AG,GG		33.2439,40.3094,42.2063	,	42/128,42/128	167893759	5475,7497	2198	4288	6486	MPC2	SO:0001819	synonymous_variant	0			-	HGNC		CCDS1266.1	1q24	2012-07-30	2012-07-30	2012-07-30	ENSG00000143158	ENSG00000143158			24515	protein-coding gene	gene with protein product		614737	"""brain protein 44"""	BRP44		3022128, 22628558	Standard	NM_015415		Approved	DKFZP564B167	uc001get.3	O95563	OTTHUMG00000034570	ENST00000367846.4:c.126C>T	1.37:g.167893759G>A		Somatic	0	34	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	42	10.64	A8K261|Q3SXR6|Q6FIF3	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_MPC	p.F42	ENST00000367846.4	37	c.126	CCDS1266.1	1																																																																																			-	pfam_MPC		0.299	MPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MPC2	protein_coding	OTTHUMT00000083652.1	G	NM_015415	rs9618		167893759	-1	no_errors	ENST00000271373	ensembl	human	known	74_37	silent	SNP	1.000	A
MEI1	150365	genome.wustl.edu	37	22	42154486	42154486	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr22:42154486G>T	ENST00000401548.3	+	18	2109	c.2069G>T	c.(2068-2070)aGa>aTa	p.R690I	MEI1_ENST00000540833.1_Missense_Mutation_p.R430I|MEI1_ENST00000400107.1_Missense_Mutation_p.R58I|MEI1_ENST00000300398.4_5'UTR|MEI1_ENST00000540880.1_Missense_Mutation_p.R8I	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						GCTCGCCAGAGACAGTACTGC	0.582																																																	0								ENSG00000167077						55.0	56.0	56.0					22																	42154486		2047	4189	6236	MEI1	SO:0001583	missense	0			-	HGNC	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.2069G>T	22.37:g.42154486G>T	ENSP00000384115:p.Arg690Ile	Somatic	0	34	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	superfamily_ARM-type_fold	p.R690I	ENST00000401548.3	37	c.2069	CCDS46718.1	22	.	.	.	.	.	.	.	.	.	.	G	18.85	3.712231	0.68730	.	.	ENSG00000167077	ENST00000401548;ENST00000540833;ENST00000400107;ENST00000540880	T;T;T;T	0.72942	3.33;3.33;-0.7;1.03	5.1	1.71	0.24356	.	0.466924	0.23354	N	0.049098	T	0.68540	0.3012	L	0.51422	1.61	0.80722	D	1	B;P;B	0.47677	0.374;0.899;0.145	B;P;B	0.51355	0.203;0.667;0.099	T	0.66224	-0.5977	10	0.62326	D	0.03	-5.3416	6.2535	0.20861	0.335:0.0:0.665:0.0	.	58;58;690	Q5TIA1-3;Q5TIA1-2;Q5TIA1	.;.;MEI1_HUMAN	I	690;430;58;8	ENSP00000384115:R690I;ENSP00000444225:R430I;ENSP00000382978:R58I;ENSP00000437436:R8I	ENSP00000382978:R58I	R	+	2	0	MEI1	40484432	0.997000	0.39634	1.000000	0.80357	0.883000	0.51084	0.294000	0.19047	0.467000	0.27218	-0.424000	0.05967	AGA	-	superfamily_ARM-type_fold		0.582	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	MEI1	protein_coding	OTTHUMT00000074937.3	G	NM_152513	-		42154486	+1	no_errors	ENST00000401548	ensembl	human	known	74_37	missense	SNP	0.999	T
SLC7A13	157724	genome.wustl.edu	37	8	87226635	87226642	+	Stop_Codon_Del	DEL	CCGACATC	CCGACATC	-	rs202114931|rs56993779|rs200509135	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	CCGACATC	CCGACATC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr8:87226635_87226642delCCGACATC	ENST00000297524.3	-	0	1516_1523				CTD-3118D11.3_ENST00000523112.1_RNA|SLC7A13_ENST00000419776.2_3'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13							integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						GTTTGCACTTCCGACATCTATTCCTCAG	0.312														968	0.193291	0.0401	0.1931	5008	,	,		18381	0.3323		0.1372	False		,,,				2504	0.3149																0								ENSG00000164893			231,4025		8,215,1905						3.0	0.0		dbSNP_129	39	992,7256		76,840,3208	no	frameshift	SLC7A13	NM_138817.2		84,1055,5113	A1A1,A1R,RR		12.0272,5.4276,9.7809				1223,11281				SLC7A13	SO:0001567	stop_retained_variant	0				HGNC	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	Exception_encountered	8.37:g.87226635_87226642delCCGACATC	Exception_encountered	Somatic	NA	NA	NA		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q05C37|Q08AH9|Q96N84	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_AA-permease/SLC12A_dom,pirsf_AA/rel_permease1	p.*471fs	ENST00000297524.3	37	c.1420_1413	CCDS34917.1	8																																																																																			-	NULL		0.312	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC7A13	protein_coding	OTTHUMT00000374704.1	CCGACATC	NM_138817			87226642	-1	no_errors	ENST00000297524	ensembl	human	known	74_37	frame_shift_del	DEL	0.020:0.001:0.000:0.000:0.000:0.001:0.001:0.000	-
GOLGA2P9	440518	genome.wustl.edu	37	19	22784767	22784769	+	RNA	DEL	AGA	AGA	-	rs376692689|rs77367148|rs138245872	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	AGA	AGA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr19:22784767_22784769delAGA	ENST00000599738.1	+	0	0				AC011467.1_ENST00000408863.1_RNA|CTC-457E21.3_ENST00000600260.1_RNA|RN7SL860P_ENST00000473738.2_RNA																							aagaaggaggagaaggagaagga	0.611														462	0.0922524	0.028	0.1369	5008	,	,		9636	0.2014		0.0596	False		,,,				2504	0.0685																0								ENSG00000269332																																			CTC-457E21.3			0				Clone_based_vega_gene																													19.37:g.22784767_22784769delAGA		Somatic	0	12	0.00		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	6	45.45		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000599738.1	37	NULL		19																																																																																			-	-		0.611	CTC-457E21.6-001	KNOWN	basic|readthrough_transcript	processed_transcript	LOC440518	processed_transcript	OTTHUMT00000464575.1	AGA				22784769	+1	no_errors	ENST00000600260	ensembl	human	known	74_37	rna	DEL	0.012:0.014:0.016	-
COX20	116228	genome.wustl.edu	37	1	245006492	245006493	+	3'UTR	INS	-	-	AGAAA	rs373567823|rs59190751|rs199795132	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:245006492_245006493insAGAAA	ENST00000411948.2	+	0	764_765				COX20_ENST00000366528.3_3'UTR|HNRNPU-AS1_ENST00000475997.1_RNA|HNRNPU-AS1_ENST00000489705.1_RNA|COX20_ENST00000498262.1_3'UTR	NM_198076.4	NP_932342.1	Q5RI15	COX20_HUMAN	COX20 cytochrome C oxidase assembly factor							integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)											ATCTTGAGCATAGAAGTCAATG	0.337														426	0.0850639	0.2126	0.049	5008	,	,		18464	0.003		0.0835	False		,,,				2504	0.0245																0								ENSG00000203667			350,3646		149,52,1797						-6.8	0.0		dbSNP_129	56	178,7968		66,46,3961	no	utr-3	FAM36A	NM_198076.4		215,98,5758	A1A1,A1R,RR		2.1851,8.7588,4.3485				528,11614				COX20	SO:0001624	3_prime_UTR_variant	0				HGNC	BC062419	CCDS31080.1	1q44	2013-05-24	2013-05-23	2012-02-24	ENSG00000203667	ENSG00000203667		"""Mitochondrial respiratory chain complex assembly factors"""	26970	protein-coding gene	gene with protein product		614698	"""family with sequence similarity 36, member A"", ""COX20 Cox2 chaperone homolog (S. cerevisiae)"""	FAM36A		22356826, 23125284	Standard	NM_198076		Approved	FLJ43269	uc001iar.3	Q5RI15	OTTHUMG00000040401	ENST00000411948.2:c.*15->AGAAA	1.37:g.245006492_245006493insAGAAA		Somatic	NA	NA	NA		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q8WV86	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000411948.2	37	NULL	CCDS31080.1	1																																																																																			-	-		0.337	COX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COX20	protein_coding	OTTHUMT00000097174.1	-	NM_198076			245006493	+1	no_errors	ENST00000391839	ensembl	human	known	74_37	rna	INS	0.000:0.000	AGAAA
SCML4	256380	genome.wustl.edu	37	6	108042142	108042142	+	Nonsense_Mutation	SNP	G	G	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr6:108042142G>T	ENST00000369020.3	-	6	983	c.738C>A	c.(736-738)taC>taA	p.Y246*	SCML4_ENST00000479803.1_5'UTR|SCML4_ENST00000369025.2_Nonsense_Mutation_p.Y4*|SCML4_ENST00000369021.3_Nonsense_Mutation_p.Y217*|SCML4_ENST00000369022.2_Nonsense_Mutation_p.Y188*	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	246					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		TGTCCACGCTGTAGCGGTTCA	0.552																																																	0								ENSG00000146285						75.0	72.0	73.0					6																	108042142		2203	4300	6503	SCML4	SO:0001587	stop_gained	0			-	HGNC		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.738C>A	6.37:g.108042142G>T	ENSP00000358016:p.Tyr246*	Somatic	0	46	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	45	8.16	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF3588	p.Y217*	ENST00000369020.3	37	c.651	CCDS5060.2	6	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354979	0.82243	.	.	ENSG00000146285	ENST00000369022;ENST00000369025;ENST00000369020;ENST00000369021	.	.	.	5.34	1.62	0.23740	.	0.490245	0.21514	N	0.073339	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.6127	0.39672	0.2857:0.0:0.7143:0.0	.	.	.	.	X	188;4;246;217	.	ENSP00000358016:Y246X	Y	-	3	2	SCML4	108148835	0.992000	0.36948	0.051000	0.19133	0.074000	0.17049	2.208000	0.42797	0.115000	0.18071	-0.145000	0.13849	TAC	-	NULL		0.552	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	SCML4	protein_coding	OTTHUMT00000041700.3	G	XM_171128	-		108042142	-1	no_errors	ENST00000369021	ensembl	human	known	74_37	nonsense	SNP	0.512	T
TBC1D2	55357	genome.wustl.edu	37	9	100961831	100961831	+	Missense_Mutation	SNP	G	G	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr9:100961831G>T	ENST00000375066.5	-	13	2677	c.2586C>A	c.(2584-2586)ttC>ttA	p.F862L	TBC1D2_ENST00000375064.1_3'UTR|TBC1D2_ENST00000342112.5_Missense_Mutation_p.F655L|TBC1D2_ENST00000375063.1_Missense_Mutation_p.F413L	NM_018421.3	NP_060891.3	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	873					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GTTTCATGCGGAAGGGGTTCA	0.632																																																	0								ENSG00000095383						135.0	138.0	137.0					9																	100961831		2203	4300	6503	TBC1D2	SO:0001583	missense	0			-	HGNC	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375066.5:c.2586C>A	9.37:g.100961831G>T	ENSP00000364207:p.Phe862Leu	Somatic	0	43	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	41	8.89	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Pleckstrin_homology,smart_Rab-GTPase-TBC_dom,pfscan_Pleckstrin_homology,pfscan_Rab-GTPase-TBC_dom	p.F862L	ENST00000375066.5	37	c.2586	CCDS35080.1	9	.	.	.	.	.	.	.	.	.	.	G	13.02	2.113382	0.37339	.	.	ENSG00000095383	ENST00000375066;ENST00000342112;ENST00000375063	T;T;T	0.22945	1.93;1.93;1.93	5.51	-9.51	0.00581	Rab-GAP/TBC domain (1);	0.121271	0.56097	D	0.000030	T	0.19604	0.0471	M	0.69185	2.1	0.27771	N	0.943501	B;B	0.31435	0.217;0.323	B;B	0.26770	0.023;0.073	T	0.25916	-1.0118	10	0.10111	T	0.7	.	19.6391	0.95749	0.3364:0.0:0.6636:0.0	.	873;862	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	L	862;655;413	ENSP00000364207:F862L;ENSP00000341567:F655L;ENSP00000364203:F413L	ENSP00000341567:F655L	F	-	3	2	TBC1D2	100001652	0.483000	0.25956	0.027000	0.17364	0.573000	0.36030	-0.417000	0.07088	-1.987000	0.00982	-1.337000	0.01257	TTC	-	superfamily_Rab-GTPase-TBC_dom		0.632	TBC1D2-002	KNOWN	basic|CCDS	protein_coding	TBC1D2	protein_coding	OTTHUMT00000053367.1	G	NM_018421	-		100961831	-1	no_errors	ENST00000375066	ensembl	human	known	74_37	missense	SNP	0.042	T
LY6G6C	80740	genome.wustl.edu	37	6	31686882	31686882	+	Silent	SNP	C	C	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr6:31686882C>A	ENST00000375819.2	-	3	534	c.369G>T	c.(367-369)ctG>ctT	p.L123L	LY6G6C_ENST00000495859.1_Silent_p.L67L	NM_025261.2	NP_079537.1	O95867	LY66C_HUMAN	lymphocyte antigen 6 complex, locus G6C	123						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|large_intestine(1)|lung(1)|skin(1)	4						CTCAGTGCAGCAGCCAGAGGC	0.612																																																	0								ENSG00000204421						72.0	65.0	68.0					6																	31686882		2203	4300	6503	LY6G6C	SO:0001819	synonymous_variant	0			-	HGNC		CCDS4714.1	6p21	2008-08-29	2002-07-29	2002-08-01	ENSG00000204421	ENSG00000204421			13936	protein-coding gene	gene with protein product		610435	"""chromosome 6 open reading frame 24"""	C6orf24		10384126, 12079290	Standard	NM_025261		Approved	G6c, NG24	uc003nwh.3	O95867	OTTHUMG00000031251	ENST00000375819.2:c.369G>T	6.37:g.31686882C>A		Somatic	0	26	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	22	15.38	Q5SRS8|Q8IY94	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.L123	ENST00000375819.2	37	c.369	CCDS4714.1	6																																																																																			-	NULL		0.612	LY6G6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LY6G6C	protein_coding	OTTHUMT00000076530.2	C		-		31686882	-1	no_errors	ENST00000375819	ensembl	human	known	74_37	silent	SNP	0.964	A
NOP9	161424	genome.wustl.edu	37	14	24769849	24769850	+	In_Frame_Ins	INS	-	-	GAGGAG	rs113258190|rs544761261|rs71119069	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr14:24769849_24769850insGAGGAG	ENST00000267425.3	+	2	576_577	c.483_484insGAGGAG	c.(484-486)gag>GAGGAGgag	p.162_162E>EEE	DHRS1_ENST00000396813.1_5'Flank|NOP9_ENST00000396802.3_In_Frame_Ins_p.162_162E>EEE|DHRS1_ENST00000288111.7_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	162	Poly-Glu.						poly(A) RNA binding (GO:0044822)	p.A161_E162insG(1)									GGAGTGCTGCAgaggaggagga	0.579																																																	1	Insertion - In frame(1)	liver(1)						ENSG00000196943																																			NOP9	SO:0001652	inframe_insertion	0				HGNC		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.502_507dupGAGGAG	14.37:g.24769850_24769855dupGAGGAG	ENSP00000267425:p.GluGlu168dup	Somatic	NA	NA	NA		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A8MY76|Q8IVF0|Q8TBS6	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	superfamily_ARM-type_fold,smart_Pumilio_RNA-bd_rpt	p.165in_frame_insEE	ENST00000267425.3	37	c.483_484	CCDS9624.1	14																																																																																			-	superfamily_ARM-type_fold		0.579	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NOP9	protein_coding	OTTHUMT00000073186.2	-				24769850	+1	no_errors	ENST00000267425	ensembl	human	known	74_37	in_frame_ins	INS	0.000:0.015	GAGGAG
ARHGEF9	23229	genome.wustl.edu	37	X	62898428	62898429	+	Frame_Shift_Ins	INS	-	-	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrX:62898428_62898429insA	ENST00000253401.6	-	5	1385_1386	c.585_586insT	c.(583-588)tctgagfs	p.E196fs	ARHGEF9_ENST00000495564.1_5'UTR|ARHGEF9_ENST00000374878.1_Frame_Shift_Ins_p.E194fs|ARHGEF9_ENST00000433323.2_5'Flank|ARHGEF9_ENST00000374870.4_Frame_Shift_Ins_p.E94fs|ARHGEF9_ENST00000374872.1_Frame_Shift_Ins_p.E175fs|ARHGEF9_ENST00000437457.2_Frame_Shift_Ins_p.E143fs	NM_015185.2	NP_056000.1	O43307	ARHG9_HUMAN	Cdc42 guanine nucleotide exchange factor (GEF) 9	196	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ion transmembrane transport (GO:0034220)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|skin(1)	35						TTACAATACTCAGAGTATATCC	0.455																																																	0								ENSG00000131089																																			ARHGEF9	SO:0001589	frameshift_variant	0				HGNC	AB007884	CCDS35315.1, CCDS55429.1, CCDS55430.1	Xq11.1	2013-01-10			ENSG00000131089	ENSG00000131089		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14561	protein-coding gene	gene with protein product	"""collybistin"""	300429				10559246, 9455477	Standard	NM_015185		Approved	KIAA0424, PEM-2	uc011mot.2	O43307	OTTHUMG00000021700	ENST00000253401.6:c.586dupT	X.37:g.62898429_62898429dupA	ENSP00000253401:p.Glu196fs	Somatic	0	25	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	21	30.00	A8K1S8|B4DHC7|F8W7P8|Q5JSL6	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_DH-domain,pfam_SH3_2,pfam_SH3_domain,pfam_Pleckstrin_homology,superfamily_DH-domain,superfamily_SH3_domain,smart_SH3_domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_DH-domain	p.E195fs	ENST00000253401.6	37	c.586_585	CCDS35315.1	X																																																																																			-	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,pfscan_DH-domain		0.455	ARHGEF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF9	protein_coding	OTTHUMT00000056937.1	-				62898429	-1	no_errors	ENST00000253401	ensembl	human	known	74_37	frame_shift_ins	INS	1.000:0.981	A
CASP5	838	genome.wustl.edu	37	11	104878041	104878041	+	Frame_Shift_Del	DEL	T	T	-	rs144697764		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr11:104878041delT	ENST00000260315.3	-	3	201	c.202delA	c.(202-204)acafs	p.T68fs	CASP5_ENST00000526056.1_Frame_Shift_Del_p.T81fs|CASP5_ENST00000444749.2_Frame_Shift_Del_p.T10fs|CASP5_ENST00000531367.1_Intron|CASP5_ENST00000393139.2_Frame_Shift_Del_p.T35fs|CASP5_ENST00000418434.1_Intron|CASP5_ENST00000393141.2_Frame_Shift_Del_p.T81fs			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	68	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)	p.T52fs*26(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		ATCTTAACTGTTTTTTTTTTG	0.358																																																	1	Deletion - Frameshift(1)	ovary(1)						ENSG00000137757		,,,	386,251,42,3585		1,0,1,383,0,0,251,0,41,1455	104.0	101.0	102.0		,,,	-2.3	0.0	11	dbSNP_132	106	651,407,1,7195		0,0,0,651,0,0,407,0,1,3068	no	codingComplex,codingComplex,intron,codingComplex	CASP5	NM_004347.3,NM_001136112.1,NM_001136110.1,NM_001136109.1	,,,	1,0,1,1034,0,0,658,0,42,4523	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		12.8301,15.924,13.884	,,,	,,,	104878041	1037,658,43,10780	2202	4299	6501	CASP5	SO:0001589	frameshift_variant	0				HGNC		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.202delA	11.37:g.104878041delT	ENSP00000260315:p.Thr68fs	Somatic	0	24	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	30	14.29	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Pept_C14_caspase,pfam_CARD,superfamily_DEATH-like_dom,smart_CARD,smart_Pept_C14A_p45_core,pirsf_Caspase_IL-1_beta,pfscan_CARD,pfscan_Pept_C14_p10,pfscan_Pept_C14_ICE_p20,prints_Pept_C14A_p45_core	p.T81fs	ENST00000260315.3	37	c.241	CCDS8328.2	11																																																																																			-	pfam_CARD,superfamily_DEATH-like_dom,smart_CARD,pirsf_Caspase_IL-1_beta,pfscan_CARD		0.358	CASP5-001	KNOWN	basic|CCDS	protein_coding	CASP5	protein_coding	OTTHUMT00000109397.2	T	NM_004347			104878041	-1	no_errors	ENST00000393141	ensembl	human	known	74_37	frame_shift_del	DEL	0.000	-
MT-ND5	4540	genome.wustl.edu	37	M	13177	13177	+	Missense_Mutation	SNP	G	G	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:13177G>A	ENST00000361567.2	+	1	841	c.841G>A	c.(841-843)Ggc>Agc	p.G281S	MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	281					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CACTATGCTTAGGCGCTATCA	0.448																																																	0								ENSG00000198786																																			MT-ND5	SO:0001583	missense	0			-	HGNC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.841G>A	M.37:g.13177G>A	ENSP00000354813:p.Gly281Ser	Somatic	0	216	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	20	23.08	Q34773|Q8WCY3	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_NADH_UbQ/plastoQ_OxRdtase,pfam_NADH_DH_su5_C,pfam_NADH_UbQ_OxRdtase_chain5/L_N,tigrfam_NADHpl_OxRdtase_5	p.G281S	ENST00000361567.2	37	c.841		MT																																																																																			-	pfam_NADH_UbQ/plastoQ_OxRdtase,tigrfam_NADHpl_OxRdtase_5		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	protein_coding		G	YP_003024036	-		13177	+1	no_errors	ENST00000361567	ensembl	human	known	74_37	missense	SNP	NULL	A
TMEM141	85014	genome.wustl.edu	37	9	139687452	139687495	+	3'UTR	DEL	CCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT	CCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT	-	rs200304774|rs369048836|rs139255997|rs549203031	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	CCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT	CCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr9:139687452_139687495delCCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT	ENST00000290079.8	+	0	511_554				TMEM141_ENST00000465017.1_3'UTR|RP11-216L13.17_ENST00000456614.2_Intron	NM_032928.3	NP_116317.1	Q96I45	TM141_HUMAN	transmembrane protein 141							integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)|prostate(1)	4	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.67e-06)|Epithelial(140;0.000112)		TGGCTGCTGCCCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCTCCCTGGGGTG	0.627														343	0.0684904	0.0749	0.0086	5008	,	,		24824	0.1319		0.0219	False		,,,				2504	0.0849																0								ENSG00000244187																																			TMEM141	SO:0001624	3_prime_UTR_variant	0				HGNC	BC007834	CCDS7007.1	9q34.3	2009-11-13			ENSG00000244187	ENSG00000244187			28211	protein-coding gene	gene with protein product							Standard	NM_032928		Approved	MGC14141	uc004cje.4	Q96I45	OTTHUMG00000020945	ENST00000290079.8:c.*211CCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT>-	9.37:g.139687452_139687495delCCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT		Somatic	NA	NA	NA		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A6NIZ7|Q5T5R5	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000290079.8	37	NULL	CCDS7007.1	9																																																																																			-	-		0.627	TMEM141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM141	protein_coding	OTTHUMT00000055119.1	CCCAACCTGGGACCTGCCCAGGAGGTTGGAGCAGAAAGGGCTCT	NM_032928			139687495	+1	no_errors	ENST00000465017	ensembl	human	known	74_37	rna	DEL	0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.003:0.010:0.014:0.025:0.055:0.074:0.106:0.128:0.137:0.122:0.015:0.004:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.008:0.042:0.050:0.053:0.036:0.005:0.000:0.000:0.000:0.002:0.000:0.000:0.000:0.001	-
LOC101927209	101927209	genome.wustl.edu	37	1	142621177	142621177	+	lincRNA	SNP	A	A	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:142621177A>T	ENST00000610091.1	-	0	6364				RP11-417J8.3_ENST00000426408.1_lincRNA																							ggaaatatacataaataagat	0.333																																																	0								ENSG00000230880																																			RP11-417J8.3			0			-	Clone_based_vega_gene																													1.37:g.142621177A>T		Somatic	0	70	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	64	11.11		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000610091.1	37	NULL		1																																																																																			-	-		0.333	RP11-417J8.6-001	KNOWN	basic	lincRNA	LOC101927209	lincRNA	OTTHUMT00000037265.2	A		-		142621177	+1	no_errors	ENST00000412092	ensembl	human	known	74_37	rna	SNP	0.029	T
KDM5B	10765	genome.wustl.edu	37	1	202709871	202709871	+	Silent	SNP	G	G	A			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr1:202709871G>A	ENST00000367265.3	-	20	4179	c.3015C>T	c.(3013-3015)ccC>ccT	p.P1005P	KDM5B_ENST00000367264.2_Silent_p.P1041P	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1005					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						CCGCACCATTGGGCAGATATG	0.453																																																	0								ENSG00000117139						80.0	82.0	82.0					1																	202709871		2203	4300	6503	KDM5B	SO:0001819	synonymous_variant	0			-	HGNC	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3015C>T	1.37:g.202709871G>A		Somatic	0	42	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	29	12.12	O95811|Q15752|Q9Y3Q5	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Lys_sp_deMease_like_dom,pfam_JmjC_dom,pfam_Znf_PHD-finger,pfam_ARID/BRIGHT_DNA-bd,pfam_Znf_C5HC2,pfam_TF_JmjN,superfamily_ARID/BRIGHT_DNA-bd,superfamily_Znf_FYVE_PHD,smart_TF_JmjN,smart_ARID/BRIGHT_DNA-bd,smart_Znf_PHD,smart_JmjC_dom,pfscan_TF_JmjN,pfscan_JmjC_dom,pfscan_Znf_PHD-finger,pfscan_ARID/BRIGHT_DNA-bd	p.P1041	ENST00000367265.3	37	c.3123	CCDS30974.1	1																																																																																			-	pfam_Lys_sp_deMease_like_dom		0.453	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KDM5B	protein_coding	OTTHUMT00000099184.2	G	NM_006618	-		202709871	-1	no_errors	ENST00000367264	ensembl	human	known	74_37	silent	SNP	1.000	A
LRBA	987	genome.wustl.edu	37	4	151186065	151186069	+	3'UTR	DEL	AACAA	AACAA	-	rs113745272|rs9307874|rs75691255	byFrequency	TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	AACAA	AACAA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr4:151186065_151186069delAACAA	ENST00000357115.3	-	0	9640_9644				LRBA_ENST00000535741.1_3'UTR|LRBA_ENST00000510413.1_3'UTR|LRBA_ENST00000503716.1_5'UTR	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing							cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					GGGGTGCCCCAACAAAACAACAGTG	0.459														2931	0.585264	0.3865	0.6974	5008	,	,		16738	0.4762		0.6501	False		,,,				2504	0.82																0								ENSG00000198589																																			LRBA	SO:0001624	3_prime_UTR_variant	0				HGNC	AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589		"""WD repeat domain containing"""	1742	protein-coding gene	gene with protein product		606453		CDC4L		1505956, 11254716	Standard	NM_006726		Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000357115.3:c.*809TTGTT>-	4.37:g.151186070_151186074delAACAA		Somatic	NA	NA	NA		0.5799845006844042	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000357115.3	37	NULL	CCDS3773.1	4																																																																																			-	-		0.459	LRBA-002	KNOWN	basic|CCDS	protein_coding	LRBA	protein_coding	OTTHUMT00000364939.1	AACAA				151186069	-1	no_errors	ENST00000503716	ensembl	human	known	74_37	rna	DEL	0.005:0.005:0.005:0.005:0.004	-
MT-ND5	4540	genome.wustl.edu	37	M	12705	12705	+	Silent	SNP	C	C	T			TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chrM:12705C>T	ENST00000361567.2	+	1	369	c.369C>T	c.(367-369)atC>atT	p.I123I	MT-TH_ENST00000387441.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	123					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TATCTACTCATTTTCCTAATT	0.373																																																	0								ENSG00000198786																																			MT-ND5	SO:0001819	synonymous_variant	0			-	HGNC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.369C>T	M.37:g.12705C>T		Somatic	0	178	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	19	20.83	Q34773|Q8WCY3	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_NADH_UbQ/plastoQ_OxRdtase,pfam_NADH_DH_su5_C,pfam_NADH_UbQ_OxRdtase_chain5/L_N,tigrfam_NADHpl_OxRdtase_5	p.I123	ENST00000361567.2	37	c.369		MT																																																																																			-	pfam_NADH_UbQ_OxRdtase_chain5/L_N,tigrfam_NADHpl_OxRdtase_5		0.373	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	MT-ND5	protein_coding		C	YP_003024036	rs2854122		12705	+1	no_errors	ENST00000361567	ensembl	human	known	74_37	silent	SNP	NULL	T
NYAP2	57624	genome.wustl.edu	37	2	226516263	226516263	+	Silent	SNP	G	G	A	rs374009602		TCGA-K1-A3PO-01A-11D-A21Q-09	TCGA-K1-A3PO-11A-12D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	11bb5036-42ef-479e-b619-46a4aa3ed5cb	b2c9d18c-b494-450b-88ea-23fd0434115e	g.chr2:226516263G>A	ENST00000272907.6	+	6	2357	c.1944G>A	c.(1942-1944)tcG>tcA	p.S648S		NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	648					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												TACCATCATCGTTAGCCAATC	0.502																																																	0								ENSG00000144460	G		1,4227		0,1,2113	242.0	244.0	243.0		1944	4.8	1.0	2		243	0,8462		0,0,4231	no	coding-synonymous	KIAA1486	NM_020864.1		0,1,6344	AA,AG,GG		0.0,0.0237,0.0079		648/654	226516263	1,12689	2114	4231	6345	NYAP2	SO:0001819	synonymous_variant	0			-	HGNC	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1944G>A	2.37:g.226516263G>A		Somatic	0	44	0.00		NA	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	10	44	18.52	A2RRN4|Q96NL2	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.S648	ENST00000272907.6	37	c.1944	CCDS46529.1	2																																																																																			-	NULL		0.502	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NYAP2	protein_coding	OTTHUMT00000331258.1	G	NM_020864	-		226516263	+1	no_errors	ENST00000272907	ensembl	human	known	74_37	silent	SNP	1.000	A
