#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ADAMTSL4	54507	genome.wustl.edu	37	1	150527109	150527109	+	Intron	SNP	T	T	C	rs12095798	byFrequency	TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr1:150527109T>C	ENST00000369038.2	+	5	1435				ADAMTSL4_ENST00000369041.5_Intron|ADAMTSL4_ENST00000369039.5_Splice_Site_p.G434G|RP11-54A4.2_ENST00000442435.2_RNA|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000271643.4_Intron			Q6UY14	ATL4_HUMAN	ADAMTS-like 4						apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			ACAGCACAGGTGGTGAGTGGT	0.632													T|||	249	0.0497204	0.1793	0.0159	5008	,	,		17991	0.0		0.001	False		,,,				2504	0.0					dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.1234+166T>C	1.37:g.150527109T>C			B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Silent	SNP	pfam_ADAM_spacer1,pfam_Thrombospondin_1_rpt,pfam_PLAC,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_PLAC,pfscan_Thrombospondin_1_rpt	p.G434	ENST00000369038.2	37	c.1302	CCDS955.1	1																																																																																			ADAMTSL4	-	NULL	ENSG00000143382		0.632	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	ADAMTSL4	HGNC	protein_coding	OTTHUMT00000084395.4	10	0.00	0	T	NM_019032		150527109	150527109	+1	no_errors	ENST00000369039	ensembl	human	known	69_37n	silent	11	42.11	8	SNP	0.001	C
BAIAP3	8938	genome.wustl.edu	37	16	1397942	1397942	+	Missense_Mutation	SNP	T	T	C			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr16:1397942T>C	ENST00000324385.5	+	32	3336	c.3178T>C	c.(3178-3180)Ttt>Ctt	p.F1060L	BAIAP3_ENST00000562208.1_Missense_Mutation_p.F1002L|BAIAP3_ENST00000397489.1_Missense_Mutation_p.F1042L|BAIAP3_ENST00000568887.1_Missense_Mutation_p.F997L|BAIAP3_ENST00000426824.3_Missense_Mutation_p.F1025L|BAIAP3_ENST00000397488.2_Missense_Mutation_p.F1042L|BAIAP3_ENST00000421665.2_Missense_Mutation_p.F989L	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	1060	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)	p.F1060L(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				ACCGCATCTCTTTCCACTGGT	0.627																																						dbGAP											1	Substitution - Missense(1)	breast(1)											59.0	65.0	63.0					16																	1397942		2198	4298	6496	-	-	-	SO:0001583	missense	0			AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.3178T>C	16.37:g.1397942T>C	ENSP00000324510:p.Phe1060Leu		A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	pfam_C2_Ca-dep,pfam_Munc13_subgr_dom-2,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,pfscan_C2_membr_targeting	p.F1060L	ENST00000324385.5	37	c.3178	CCDS10434.1	16	.	.	.	.	.	.	.	.	.	.	T	20.4	3.989507	0.74589	.	.	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58	5.01	5.01	0.66863	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.81791	0.4897	M	0.72353	2.195	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.96;0.997;0.997;0.997	T	0.81805	-0.0764	10	0.41790	T	0.15	-32.3096	12.668	0.56853	0.0:0.0:0.0:1.0	.	989;1002;1060;1042	E7EUB9;B4DIK3;O94812;A2A2B2	.;.;BAIP3_HUMAN;.	L	1025;1042;1060;1042;989	ENSP00000407242:F1025L;ENSP00000380625:F1042L;ENSP00000324510:F1060L;ENSP00000380626:F1042L;ENSP00000409533:F989L	ENSP00000324510:F1060L	F	+	1	0	BAIAP3	1337943	1.000000	0.71417	0.977000	0.42913	0.594000	0.36715	4.291000	0.59025	1.885000	0.54596	0.459000	0.35465	TTT	BAIAP3	-	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,pfscan_C2_membr_targeting	ENSG00000007516		0.627	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	BAIAP3	HGNC	protein_coding	OTTHUMT00000109056.3	8	0.00	0	T			1397942	1397942	+1	no_errors	ENST00000324385	ensembl	human	known	69_37n	missense	18	25.00	6	SNP	1.000	C
CALD1	800	genome.wustl.edu	37	7	134645312	134645312	+	Missense_Mutation	SNP	C	C	A			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr7:134645312C>A	ENST00000361675.2	+	13	2457	c.2228C>A	c.(2227-2229)tCt>tAt	p.S743Y	CALD1_ENST00000361901.2_Missense_Mutation_p.S488Y|CALD1_ENST00000361388.2_Missense_Mutation_p.S514Y|CALD1_ENST00000417172.1_Missense_Mutation_p.S488Y|CALD1_ENST00000393118.2_Missense_Mutation_p.S508Y|CALD1_ENST00000466704.1_3'UTR|CALD1_ENST00000424922.1_Missense_Mutation_p.S482Y|CALD1_ENST00000495522.1_Missense_Mutation_p.S507Y|CALD1_ENST00000422748.1_Missense_Mutation_p.S513Y|CALD1_ENST00000543443.1_Missense_Mutation_p.S493Y			Q05682	CALD1_HUMAN	caldesmon 1	743					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)	p.S743Y(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						GTAGGGGTTTCTAGCCGCATC	0.403																																						dbGAP											1	Substitution - Missense(1)	breast(1)											99.0	95.0	97.0					7																	134645312		2203	4300	6503	-	-	-	SO:0001583	missense	0			M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.2228C>A	7.37:g.134645312C>A	ENSP00000354826:p.Ser743Tyr		A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	pfam_Caldesmon_LSP,prints_Caldesmon	p.S514Y	ENST00000361675.2	37	c.1541	CCDS5835.1	7	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623343	0.87460	.	.	ENSG00000122786	ENST00000417172;ENST00000361388;ENST00000422748;ENST00000432646;ENST00000361675;ENST00000361901;ENST00000393118;ENST00000424922;ENST00000495522;ENST00000543443	T;T;T;T;T;T;T;T;T	0.56444	0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46	5.56	5.56	0.83823	.	0.000000	0.49916	D	0.000129	T	0.75874	0.3909	M	0.81682	2.555	0.47994	D	0.99956	D;D;D;D;D;D;D;D;D	0.76494	0.999;0.998;0.999;0.999;0.999;0.999;0.999;0.998;0.999	D;D;D;D;D;D;D;D;D	0.83275	0.994;0.99;0.996;0.996;0.993;0.993;0.985;0.99;0.996	T	0.78687	-0.2107	10	0.87932	D	0	-10.5772	19.5128	0.95151	0.0:1.0:0.0:0.0	.	437;493;513;507;482;508;488;514;743	B4DPW5;F5H1Z9;A8K0X1;E7EX44;Q05682-5;Q05682-3;Q05682-4;Q05682-2;Q05682	.;.;.;.;.;.;.;.;CALD1_HUMAN	Y	488;514;513;121;743;488;508;482;507;493	ENSP00000398826:S488Y;ENSP00000355000:S514Y;ENSP00000395710:S513Y;ENSP00000354826:S743Y;ENSP00000354513:S488Y;ENSP00000376826:S508Y;ENSP00000393621:S482Y;ENSP00000419673:S507Y;ENSP00000445641:S493Y	ENSP00000355000:S514Y	S	+	2	0	CALD1	134295852	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.907000	0.75724	2.607000	0.88179	0.655000	0.94253	TCT	CALD1	-	pfam_Caldesmon_LSP,prints_Caldesmon	ENSG00000122786		0.403	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	CALD1	HGNC	protein_coding	OTTHUMT00000339939.1	93	0.00	0	C	NM_033138		134645312	134645312	+1	no_errors	ENST00000361388	ensembl	human	known	69_37n	missense	119	35.83	67	SNP	1.000	A
CDK5RAP2	55755	genome.wustl.edu	37	9	123239714	123239714	+	Silent	SNP	T	T	A			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr9:123239714T>A	ENST00000349780.4	-	15	1820	c.1641A>T	c.(1639-1641)tcA>tcT	p.S547S	CDK5RAP2_ENST00000360190.4_Silent_p.S547S|CDK5RAP2_ENST00000359309.3_Silent_p.S547S|CDK5RAP2_ENST00000360822.3_Silent_p.S547S	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	547					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.S547S(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						CATAGTCTGATGATTGTTTCT	0.378											OREG0019439	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											1	Substitution - coding silent(1)	breast(1)											209.0	180.0	190.0					9																	123239714		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.1641A>T	9.37:g.123239714T>A		1525	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	pfam_Spindle_assoc	p.S547	ENST00000349780.4	37	c.1641	CCDS6823.1	9																																																																																			CDK5RAP2	-	NULL	ENSG00000136861		0.378	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CDK5RAP2	HGNC	protein_coding	OTTHUMT00000055535.1	203	0.00	0	T	NM_018249		123239714	123239714	-1	no_errors	ENST00000349780	ensembl	human	known	69_37n	silent	211	34.47	111	SNP	0.998	A
CTCF	10664	genome.wustl.edu	37	16	67645853	67645854	+	Splice_Site	INS	-	-	TAC			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr16:67645853_67645854insTAC	ENST00000264010.4	+	4	1225_1226		c.e4-1		AC009095.4_ENST00000388909.4_RNA|CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)						chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.G261>VR(1)		breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		TTTGCACATAGGTGTAAAGAAG	0.356																																					Colon(175;1200 1966 6945 23069 27405)	dbGAP											1	Complex - insertion inframe(1)	breast(1)																																								-	-	-	SO:0001630	splice_region_variant	0			U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"""Zinc fingers, C2H2-type"""	13723	protein-coding gene	gene with protein product	"""11 zinc finger transcriptional repressor"""	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.782-1->TAC	16.37:g.67645853_67645854insTAC			B5MC38|Q53XI7|Q59EL8	Splice_Site	INS	-	e2-1	ENST00000264010.4	37	c.782-1_782-1	CCDS10841.1	16																																																																																			CTCF	-	-	ENSG00000102974		0.356	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CTCF	HGNC	protein_coding	OTTHUMT00000268870.2	61	0.00	0	-	NM_006565	Intron	67645853	67645854	+1	no_errors	ENST00000264010	ensembl	human	known	69_37n	splice_site_ins	40	56.04	51	INS	1.000:1.000	TAC
SMIM10	644538	genome.wustl.edu	37	X	134125278	134125278	+	Silent	SNP	C	C	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chrX:134125278C>T	ENST00000330288.4	+	1	311	c.153C>T	c.(151-153)ctC>ctT	p.L51L		NM_001163438.1	NP_001156910.1	Q96HG1	SIM10_HUMAN	small integral membrane protein 10	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L51L(2)									GCACGCTGCTCACCTTCTTCG	0.622																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											36.0	35.0	35.0					X																	134125278		692	1591	2283	-	-	-	SO:0001819	synonymous_variant	0				CCDS55502.1	Xq26.3	2012-11-29	2012-11-29	2012-11-29	ENSG00000184785	ENSG00000184785			41913	protein-coding gene	gene with protein product			"""chromosome X open reading frame 69"""	CXorf69			Standard	NM_001163438		Approved		uc011mvs.2	Q96HG1		ENST00000330288.4:c.153C>T	X.37:g.134125278C>T				Silent	SNP	NULL	p.L51	ENST00000330288.4	37	c.153	CCDS55502.1	X																																																																																			CXorf69	-	NULL	ENSG00000184785		0.622	SMIM10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	CXorf69	HGNC	protein_coding		11	0.00	0	C	NM_001163438		134125278	134125278	+1	no_errors	ENST00000330288	ensembl	human	known	69_37n	silent	40	46.67	35	SNP	0.998	T
CYP27A1	1593	genome.wustl.edu	37	2	219647024	219647024	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr2:219647024C>T	ENST00000258415.4	+	1	546	c.119C>T	c.(118-120)gCc>gTc	p.A40V		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	40					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)	p.A40V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	TCGGACAAGGCCACCGGAGCT	0.711																																						dbGAP											1	Substitution - Missense(1)	breast(1)											22.0	21.0	22.0					2																	219647024		2197	4291	6488	-	-	-	SO:0001583	missense	0			BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"""Cytochrome P450s"""	2605	protein-coding gene	gene with protein product	"""cerebrotendinous xanthomatosis"""	606530	"""cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"""	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.119C>T	2.37:g.219647024C>T	ENSP00000258415:p.Ala40Val		A8K303|Q6LDB4|Q86YQ6	Missense_Mutation	SNP	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-I,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450	p.A40V	ENST00000258415.4	37	c.119	CCDS2423.1	2	.	.	.	.	.	.	.	.	.	.	C	12.51	1.959596	0.34565	.	.	ENSG00000135929	ENST00000258415	T	0.75821	-0.97	3.62	0.377	0.16198	.	0.494534	0.19531	N	0.112029	T	0.48677	0.1513	N	0.14661	0.345	0.09310	N	1	B	0.30068	0.267	B	0.22386	0.039	T	0.29792	-1.0000	10	0.31617	T	0.26	-0.8548	5.4683	0.16656	0.0:0.4576:0.4165:0.126	.	40	Q02318	CP27A_HUMAN	V	40	ENSP00000258415:A40V	ENSP00000258415:A40V	A	+	2	0	CYP27A1	219355268	0.000000	0.05858	0.016000	0.15963	0.054000	0.15201	-0.061000	0.11693	0.151000	0.19162	0.313000	0.20887	GCC	CYP27A1	-	NULL	ENSG00000135929		0.711	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP27A1	HGNC	protein_coding	OTTHUMT00000109734.4	13	0.00	0	C			219647024	219647024	+1	no_errors	ENST00000258415	ensembl	human	known	69_37n	missense	24	41.46	17	SNP	0.001	T
CYTH4	27128	genome.wustl.edu	37	22	37707034	37707034	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr22:37707034C>T	ENST00000248901.6	+	10	1001	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C		NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	272	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Phosphatidylinositol 3,4,5-trisphosphate binding. {ECO:0000250}.				positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)	p.R272C(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						CGCAGGGGGCCGCGTGAAGAC	0.617																																						dbGAP											1	Substitution - Missense(1)	breast(1)											145.0	121.0	129.0					22																	37707034		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"""Pleckstrin homology (PH) domain containing"""	9505	protein-coding gene	gene with protein product		606514	"""pleckstrin homology, Sec7 and coiled/coil domains 4"", ""pleckstrin homology, Sec7 and coiled-coil domains 4"""	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.814C>T	22.37:g.37707034C>T	ENSP00000248901:p.Arg272Cys		Q5R3F9|Q9UGT6	Missense_Mutation	SNP	pfam_Sec7,pfam_Pleckstrin_homology,superfamily_Sec7,smart_Sec7,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_Sec7	p.R272C	ENST00000248901.6	37	c.814	CCDS13946.1	22	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.93|18.93	3.727890|3.727890	0.69074|0.69074	.|.	.|.	ENSG00000100055|ENSG00000100055	ENST00000446506|ENST00000248901	.|T	.|0.76316	.|-1.01	4.52|4.52	3.37|3.37	0.38596|0.38596	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.88418|0.88418	0.6431|0.6431	M|M	0.90705|0.90705	3.14|3.14	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.73380	.|0.98	D|D	0.89923|0.89923	0.4060|0.4060	5|10	.|0.72032	.|D	.|0.01	.|.	11.3314|11.3314	0.49479|0.49479	0.2544:0.7456:0.0:0.0|0.2544:0.7456:0.0:0.0	.|.	.|272	.|Q9UIA0	.|CYH4_HUMAN	L|C	24|272	.|ENSP00000248901:R272C	.|ENSP00000248901:R272C	P|R	+|+	2|1	0|0	CYTH4|CYTH4	36036980|36036980	0.008000|0.008000	0.16893|0.16893	0.998000|0.998000	0.56505|0.56505	0.979000|0.979000	0.70002|0.70002	0.109000|0.109000	0.15417|0.15417	2.200000|2.200000	0.70718|0.70718	0.655000|0.655000	0.94253|0.94253	CCG|CGC	CYTH4	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	ENSG00000100055		0.617	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYTH4	HGNC	protein_coding	OTTHUMT00000318917.1	18	0.00	0	C			37707034	37707034	+1	no_errors	ENST00000248901	ensembl	human	known	69_37n	missense	41	16.33	8	SNP	1.000	T
DNM1P46	196968	genome.wustl.edu	37	15	100331916	100331916	+	RNA	SNP	C	C	A			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr15:100331916C>A	ENST00000341853.1	-	0	2275				AC090825.1_ENST00000408584.1_RNA|RN7SL484P_ENST00000462651.2_RNA	NR_003260.1		Q6ZS02	DMP46_HUMAN	DNM1 pseudogene 46							microtubule (GO:0005874)	GTPase activity (GO:0003924)										CCTTTATGCTCTTGGTTTCCC	0.572																																						dbGAP											0													42.0	43.0	43.0					15																	100331916		876	1991	2867	-	-	-			0			AJ576275		15q26.3	2013-04-25			ENSG00000182397	ENSG00000182397			35199	pseudogene	pseudogene			"""chromosome 15 open reading frame 51"""	DNM1DN14@, C15orf51			Standard	NR_003260		Approved	DNM1DN14.2, FLJ45937, DKFZp434I1020	uc021sxl.1	Q6ZS02	OTTHUMG00000149852		15.37:g.100331916C>A			Q3ZCN3	RNA	SNP	-	NULL	ENST00000341853.1	37	NULL		15																																																																																			DNM1P46	-	-	ENSG00000182397		0.572	DNM1P46-002	KNOWN	basic	processed_transcript	DNM1P46	HGNC	pseudogene	OTTHUMT00000313543.1	14	0.00	0	C	NR_003260		100331916	100331916	-1	no_errors	ENST00000341853	ensembl	human	known	69_37n	rna	32	27.27	12	SNP	0.605	A
FAM117B	150864	genome.wustl.edu	37	2	203630190	203630190	+	Silent	SNP	C	C	A			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr2:203630190C>A	ENST00000392238.2	+	8	1473	c.1473C>A	c.(1471-1473)atC>atA	p.I491I	FAM117B_ENST00000303116.6_Silent_p.I247I			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	491								p.I247I(1)|p.I491I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						TTCATGAAATCCCAGCCTTTT	0.388																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											100.0	105.0	103.0					2																	203630190		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"""	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.1473C>A	2.37:g.203630190C>A			Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Silent	SNP	NULL	p.I491	ENST00000392238.2	37	c.1473	CCDS33362.2	2																																																																																			FAM117B	-	NULL	ENSG00000138439		0.388	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FAM117B	HGNC	protein_coding	OTTHUMT00000335888.3	39	0.00	0	C	NM_173511		203630190	203630190	+1	no_errors	ENST00000392238	ensembl	human	known	69_37n	silent	82	25.45	28	SNP	0.999	A
FAM157B	100132403	genome.wustl.edu	37	9	141107536	141107537	+	lincRNA	INS	-	-	GCA	rs367832601|rs554298933|rs370981092		TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr9:141107536_141107537insGCA	ENST00000446912.2	+	0	19_20							P0CG42	F157B_HUMAN	family with sequence similarity 157, member B																		CGgcagcggcggcagcagcagc	0.545																																						dbGAP											0																																										-	-	-			0					9q34	2013-01-24			ENSG00000233013	ENSG00000233013			34080	other	unknown							Standard	NM_001145249		Approved		uc011mfe.1	P0CG42	OTTHUMG00000021000		9.37:g.141107543_141107545dupGCA				RNA	INS	-	NULL	ENST00000446912.2	37	NULL		9																																																																																			FAM157B	-	-	ENSG00000233013		0.545	FAM157B-001	KNOWN	mRNA_end_NF|basic	lincRNA	FAM157B	HGNC	lincRNA	OTTHUMT00000055378.2	28	0.00	0	-	NM_001145249		141107536	141107537	+1	no_errors	ENST00000446912	ensembl	human	known	69_37n	rna	68	13.92	11	INS	0.033:0.036	GCA
GPR160	26996	genome.wustl.edu	37	3	169802155	169802155	+	Missense_Mutation	SNP	T	T	A	rs201952152		TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr3:169802155T>A	ENST00000355897.5	+	4	1003	c.395T>A	c.(394-396)tTt>tAt	p.F132Y		NM_014373.2	NP_055188.1	Q9UJ42	GP160_HUMAN	G protein-coupled receptor 160	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.F132Y(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)	8	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			AAGCTTTCATTTAAGTGTCAA	0.323																																						dbGAP											1	Substitution - Missense(1)	breast(1)											37.0	40.0	39.0					3																	169802155		2199	4294	6493	-	-	-	SO:0001583	missense	0			AB083583	CCDS3211.1	3q26.2-q27	2012-08-21			ENSG00000173890	ENSG00000173890		"""GPCR / Class A : Orphans"""	23693	protein-coding gene	gene with protein product						12044878	Standard	NM_014373		Approved	GPCR150, GPCR1	uc003fgi.3	Q9UJ42	OTTHUMG00000158776	ENST00000355897.5:c.395T>A	3.37:g.169802155T>A	ENSP00000348161:p.Phe132Tyr		D3DNQ2	Missense_Mutation	SNP	pfscan_GPCR_Rhodpsn_supfam	p.F132Y	ENST00000355897.5	37	c.395	CCDS3211.1	3	.	.	.	.	.	.	.	.	.	.	T	0.766	-0.767405	0.02974	.	.	ENSG00000173890	ENST00000355897;ENST00000485735;ENST00000473675	T	0.14144	2.53	5.8	-2.69	0.06022	GPCR, rhodopsin-like superfamily (1);	1.056470	0.07328	N	0.878701	T	0.06872	0.0175	L	0.36672	1.1	0.09310	N	1	B	0.30973	0.302	B	0.30495	0.116	T	0.34104	-0.9842	10	0.02654	T	1	.	0.8345	0.01137	0.3138:0.2997:0.2119:0.1746	.	132	Q9UJ42	GP160_HUMAN	Y	132	ENSP00000348161:F132Y	ENSP00000348161:F132Y	F	+	2	0	GPR160	171284849	0.000000	0.05858	0.003000	0.11579	0.642000	0.38348	-1.961000	0.01516	-0.163000	0.10946	0.528000	0.53228	TTT	GPR160	-	pfscan_GPCR_Rhodpsn_supfam	ENSG00000173890		0.323	GPR160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR160	HGNC	protein_coding	OTTHUMT00000352167.1	131	0.00	0	T	NM_014373		169802155	169802155	+1	no_errors	ENST00000355897	ensembl	human	known	69_37n	missense	61	34.74	33	SNP	0.000	A
HDAC8	55869	genome.wustl.edu	37	X	71571588	71571588	+	Missense_Mutation	SNP	A	A	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chrX:71571588A>T	ENST00000373573.3	-	10	1447	c.1106T>A	c.(1105-1107)aTc>aAc	p.I369N	HDAC8_ENST00000429103.2_Missense_Mutation_p.I174N|HDAC8_ENST00000373583.1_Intron|HDAC8_ENST00000373589.4_Missense_Mutation_p.I278N	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	369					chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cohesin localization to chromatin (GO:0071922)|sister chromatid cohesion (GO:0007062)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)	p.I369N(1)		breast(3)|cervix(1)|endometrium(1)|lung(4)|prostate(1)	10	Renal(35;0.156)				Vorinostat(DB02546)	CTCACCTTTGATGTAGTTGAG	0.532																																						dbGAP											1	Substitution - Missense(1)	breast(1)											216.0	149.0	172.0					X																	71571588		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF230097	CCDS14420.1, CCDS55448.1, CCDS55449.1, CCDS55450.1, CCDS55451.1, CCDS55452.1	Xq13	2014-01-29	2002-09-02	2002-09-06	ENSG00000147099	ENSG00000147099			13315	protein-coding gene	gene with protein product		300269	"""histone deacetylase-like 1"", ""Wilson-Turner X-linked mental retardation syndrome"""	HDACL1, WTS, MRXS6		10756090, 10922473, 22889856	Standard	NM_001166448		Approved	RPD3	uc004eau.3	Q9BY41	OTTHUMG00000021814	ENST00000373573.3:c.1106T>A	X.37:g.71571588A>T	ENSP00000362674:p.Ile369Asn		A6ND12|A6ND61|A6NET3|A6NJR3|A8MQ62|B4DKN0|B4DV22|Q86VC8|Q9NP76|Q9NYH4	Missense_Mutation	SNP	pfam_His_deacetylse_dom,pirsf_His_deacetylse_1,prints_His_deacetylse_1,prints_His_deacetylse	p.I369N	ENST00000373573.3	37	c.1106	CCDS14420.1	X	.	.	.	.	.	.	.	.	.	.	A	19.16	3.774173	0.69992	.	.	ENSG00000147099	ENST00000373573;ENST00000373589;ENST00000429103	D;D;D	0.82619	-1.63;-1.63;-1.63	4.79	4.79	0.61399	Histone deacetylase domain (1);	0.046662	0.85682	D	0.000000	D	0.90738	0.7093	M	0.84511	2.7	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71184	0.972;0.919	D	0.91934	0.5557	10	0.87932	D	0	-11.2427	11.7674	0.51939	1.0:0.0:0.0:0.0	.	278;369	B4DKN0;Q9BY41	.;HDAC8_HUMAN	N	369;278;174	ENSP00000362674:I369N;ENSP00000362691:I278N;ENSP00000388459:I174N	ENSP00000362674:I369N	I	-	2	0	HDAC8	71488313	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	6.581000	0.74045	1.857000	0.53885	0.356000	0.21956	ATC	HDAC8	-	pirsf_His_deacetylse_1	ENSG00000147099		0.532	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HDAC8	HGNC	protein_coding	OTTHUMT00000057193.2	89	0.00	0	A	NM_018486		71571588	71571588	-1	no_errors	ENST00000373573	ensembl	human	known	69_37n	missense	243	35.79	136	SNP	1.000	T
IMPG1	3617	genome.wustl.edu	37	6	76640790	76640790	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr6:76640790G>A	ENST00000369950.3	-	15	2312	c.2123C>T	c.(2122-2124)gCg>gTg	p.A708V	IMPG1_ENST00000369963.3_3'UTR|Y_RNA_ENST00000363170.1_RNA	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1									p.A708V(1)		breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				GCGACACTCCGCTTCCTCAGT	0.562																																					Pancreas(37;839 1141 2599 26037)	dbGAP											1	Substitution - Missense(1)	breast(1)											107.0	85.0	93.0					6																	76640790		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2123C>T	6.37:g.76640790G>A	ENSP00000358966:p.Ala708Val			Missense_Mutation	SNP	pfam_SEA,smart_SEA,pfscan_EG-like_dom,pfscan_SEA	p.A708V	ENST00000369950.3	37	c.2123	CCDS4985.1	6	.	.	.	.	.	.	.	.	.	.	G	14.57	2.575066	0.45902	.	.	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.32272	1.74;1.46	5.45	1.74	0.24563	Epidermal growth factor-like, type 3 (1);	0.411437	0.21614	N	0.071755	T	0.33585	0.0868	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.07501	-1.0769	10	0.45353	T	0.12	.	9.1989	0.37246	0.2857:0.0:0.7143:0.0	.	708	Q17R60	IMPG1_HUMAN	V	708;69	ENSP00000358966:A708V;ENSP00000358968:A69V	ENSP00000358966:A708V	A	-	2	0	IMPG1	76697510	1.000000	0.71417	0.037000	0.18230	0.186000	0.23388	4.108000	0.57817	0.028000	0.15324	-0.677000	0.03784	GCG	IMPG1	-	pfscan_EG-like_dom	ENSG00000112706		0.562	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IMPG1	HGNC	protein_coding	OTTHUMT00000041288.1	31	0.00	0	G	NM_001563		76640790	76640790	-1	no_errors	ENST00000369950	ensembl	human	known	69_37n	missense	99	38.12	61	SNP	0.876	A
LRRC37A4P	55073	genome.wustl.edu	37	17	43592232	43592232	+	RNA	SNP	G	G	A			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr17:43592232G>A	ENST00000579913.1	-	0	290				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		TGTAGATGGCGTTTCCCGCTA	0.587																																						dbGAP											0																																										-	-	-			0			AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43592232G>A				RNA	SNP	-	NULL	ENST00000579913.1	37	NULL		17																																																																																			LRRC37A4P	-	-	ENSG00000214425		0.587	LRRC37A4P-002	KNOWN	basic	processed_transcript	LRRC37A4P	HGNC	pseudogene	OTTHUMT00000445300.1	13	0.00	0	G	NR_002940		43592232	43592232	-1	no_errors	ENST00000579913	ensembl	human	known	69_37n	rna	16	30.43	7	SNP	0.000	A
MAP3K1	4214	genome.wustl.edu	37	5	56181812	56181814	+	In_Frame_Del	DEL	GTT	GTT	-			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	GTT	GTT					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr5:56181812_56181814delGTT	ENST00000399503.3	+	17	4036_4038	c.4036_4038delGTT	c.(4036-4038)gttdel	p.V1346del		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1346	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.V1183delV(1)|p.V1346delV(1)		NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		AGAATCAGTAGTTATTAACTACA	0.345																																						dbGAP											2	Deletion - In frame(2)	breast(2)																																								-	-	-	SO:0001651	inframe_deletion	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.4036_4038delGTT	5.37:g.56181812_56181814delGTT	ENSP00000382423:p.Val1346del			In_Frame_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.V1346in_frame_del	ENST00000399503.3	37	c.4036_4038	CCDS43318.1	5																																																																																			MAP3K1	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000095015		0.345	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	139	0.00	0	GTT	XM_042066		56181812	56181814	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	in_frame_del	104	31.45	50	DEL	0.983:1.000:0.998	-
NBPF14	25832	genome.wustl.edu	37	1	145293269	145293269	+	Splice_Site	SNP	G	G	A	rs61350760		TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr1:145293269G>A	ENST00000468030.1	+	5	1125		c.e5+1		NBPF10_ENST00000369338.1_Splice_Site|NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000342960.5_5'Flank																							TTTCACAACAGTAAGTTAAGA	0.423																																						dbGAP											0																																										-	-	-	SO:0001630	splice_region_variant	0																														ENST00000468030.1:c.714+1G>A	1.37:g.145293269G>A				Splice_Site	SNP	-	e0+1	ENST00000468030.1	37	c.1+1		1																																																																																			NBPF10	-	-	ENSG00000163386		0.423	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NBPF10	HGNC	protein_coding	OTTHUMT00000038553.9	31	0.00	0	G		Intron	145293269	145293269	+1	no_errors	ENST00000369338	ensembl	human	known	69_37n	splice_site	110	14.06	18	SNP	0.024	A
MNDA	4332	genome.wustl.edu	37	1	158817523	158817523	+	Silent	SNP	C	C	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr1:158817523C>T	ENST00000368141.4	+	6	1254	c.993C>T	c.(991-993)agC>agT	p.S331S		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	331	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S331S(1)		NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					TGCAGAAAAGCGTACACAAGA	0.368																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											97.0	95.0	96.0					1																	158817523		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.993C>T	1.37:g.158817523C>T				Missense_Mutation	SNP	pfam_HIN200/IF120x,pfscan_HIN200/IF120x	p.R37C	ENST00000368141.4	37	c.109	CCDS1177.1	1	.	.	.	.	.	.	.	.	.	.	C	2.696	-0.271999	0.05716	.	.	ENSG00000163563	ENST00000438394	.	.	.	4.15	0.152	0.14893	.	.	.	.	.	T	0.07503	0.0189	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33523	-0.9865	4	.	.	.	0.0539	1.0512	0.01580	0.5045:0.2009:0.1098:0.1848	.	.	.	.	C	37	.	.	R	+	1	0	MNDA	157084147	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.772000	0.04694	0.236000	0.21180	-0.388000	0.06559	CGT	MNDA	-	pfam_HIN200/IF120x,pfscan_HIN200/IF120x	ENSG00000163563		0.368	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MNDA	HGNC	protein_coding	OTTHUMT00000059069.1	56	0.00	0	C	NM_002432		158817523	158817523	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000438394	ensembl	human	known	69_37n	missense	75	33.63	38	SNP	0.000	T
PDE12	201626	genome.wustl.edu	37	3	57543003	57543003	+	Silent	SNP	T	T	C			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr3:57543003T>C	ENST00000311180.8	+	1	1000	c.897T>C	c.(895-897)tcT>tcC	p.S299S	PDE12_ENST00000487257.1_Silent_p.S299S	NM_177966.5	NP_808881.3	Q6L8Q7	PDE12_HUMAN	phosphodiesterase 12	299					mRNA processing (GO:0006397)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)	p.S299S(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(4)|lung(3)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127)		GCACTGTCTCTTACAACATCC	0.582																																					Colon(125;308 1634 19198 50622 50717)	dbGAP											1	Substitution - coding silent(1)	breast(1)											88.0	85.0	86.0					3																	57543003		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK074423	CCDS33772.1	3p14.3	2013-10-11			ENSG00000174840	ENSG00000174840			25386	protein-coding gene	gene with protein product	"""2'-phosphodiesterase"""					15231837	Standard	NM_177966		Approved	DKFZp667B1218, 2'-PDE	uc003diw.4	Q6L8Q7	OTTHUMG00000158599	ENST00000311180.8:c.897T>C	3.37:g.57543003T>C			B4DTU8|Q8IYU3|Q8NDU2|Q8TE78	Silent	SNP	pfam_Endo/exonuclease/phosphatase,superfamily_Endo/exonuclease/phosphatase	p.S299	ENST00000311180.8	37	c.897	CCDS33772.1	3																																																																																			PDE12	-	pfam_Endo/exonuclease/phosphatase,superfamily_Endo/exonuclease/phosphatase	ENSG00000174840		0.582	PDE12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDE12	HGNC	protein_coding	OTTHUMT00000351440.2	17	0.00	0	T	NM_177966		57543003	57543003	+1	no_errors	ENST00000311180	ensembl	human	known	69_37n	silent	28	50.88	29	SNP	0.937	C
OR5K4	403278	genome.wustl.edu	37	3	98073612	98073612	+	Silent	SNP	T	T	C			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr3:98073612T>C	ENST00000354924.2	+	1	915	c.915T>C	c.(913-915)taT>taC	p.Y305Y	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	305						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y305Y(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TGAGGAATTATAACATTCTTA	0.229																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											66.0	83.0	77.0					3																	98073612		2156	4239	6395	-	-	-	SO:0001819	synonymous_variant	0				CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"""GPCR / Class A : Olfactory receptors"""	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.915T>C	3.37:g.98073612T>C				Silent	SNP	pfam_7TM_GPCR_Rhodpsn,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam	p.Y305	ENST00000354924.2	37	c.915	CCDS33802.1	3																																																																																			OR5K4	-	NULL	ENSG00000196098		0.229	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5K4	HGNC	protein_coding	OTTHUMT00000359114.1	58	0.00	0	T			98073612	98073612	+1	no_errors	ENST00000354924	ensembl	human	known	69_37n	silent	13	61.76	21	SNP	0.001	C
PIP5K1C	23396	genome.wustl.edu	37	19	3633459	3633460	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr19:3633459_3633460insG	ENST00000335312.3	-	17	2067_2068	c.1979_1980insC	c.(1978-1980)ccgfs	p.P660fs	PIP5K1C_ENST00000539785.1_Intron	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	660	Mediates interaction with TLN2.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)	p.P660fs*>9(1)		large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		CGTCGGAGGCCGGGGGGGCCTG	0.698																																					Esophageal Squamous(135;99 1744 12852 27186 39851)	dbGAP											1	Deletion - Frameshift(1)	ovary(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1980dupC	19.37:g.3633466_3633466dupG	ENSP00000335333:p.Pro660fs		B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Frame_Shift_Ins	INS	pfam_PInositol-4-P-5-kinase_core,smart_PInositol-4P-5-kinase_core_sub	p.A661fs	ENST00000335312.3	37	c.1980_1979	CCDS32872.1	19																																																																																			PIP5K1C	-	NULL	ENSG00000186111		0.698	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PIP5K1C	HGNC	protein_coding	OTTHUMT00000453432.2	10	0.00	0	-	NM_012398		3633459	3633460	-1	no_errors	ENST00000335312	ensembl	human	known	69_37n	frame_shift_ins	15	25.00	5	INS	0.922:0.997	G
RBBP6	5930	genome.wustl.edu	37	16	24567190	24567190	+	Silent	SNP	C	C	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr16:24567190C>T	ENST00000319715.4	+	6	918	c.486C>T	c.(484-486)ttC>ttT	p.F162F	RBBP6_ENST00000348022.2_Silent_p.F162F|RBBP6_ENST00000381039.3_Silent_p.F162F	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	162					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F162F(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		ACACGTGTTTCCGTTGTGGTA	0.358																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											81.0	78.0	79.0					16																	24567190		2197	4300	6497	-	-	-	SO:0001819	synonymous_variant	0				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.486C>T	16.37:g.24567190C>T			Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	pfam_DWNN_domain,pfam_Ubox_domain,pfam_Znf_CCHC,superfamily_Znf_CCHC,smart_Znf_CCHC,smart_Znf_RING,pfscan_Znf_RING,pfscan_Znf_CCHC	p.F162	ENST00000319715.4	37	c.486	CCDS10621.1	16																																																																																			RBBP6	-	pfam_Znf_CCHC,superfamily_Znf_CCHC,smart_Znf_CCHC,pfscan_Znf_CCHC	ENSG00000122257		0.358	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBBP6	HGNC	protein_coding	OTTHUMT00000214067.2	120	0.00	0	C	NM_006910		24567190	24567190	+1	no_errors	ENST00000319715	ensembl	human	known	69_37n	silent	167	23.74	52	SNP	0.998	T
REG1A	5967	genome.wustl.edu	37	2	79350284	79350284	+	Silent	SNP	A	A	G			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr2:79350284A>G	ENST00000233735.1	+	6	547	c.444A>G	c.(442-444)aaA>aaG	p.K148K		NM_002909.4	NP_002900.2	P05451	REG1A_HUMAN	regenerating islet-derived 1 alpha	148	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|growth factor activity (GO:0008083)	p.K148K(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(26)|prostate(1)|upper_aerodigestive_tract(1)	39						GATTCCAGAAATGGAAGGATG	0.423																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											89.0	88.0	88.0					2																	79350284		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS1964.1	2p12	2008-09-04	2008-06-04		ENSG00000115386	ENSG00000115386			9951	protein-coding gene	gene with protein product	"""pancreatic stone protein"", ""pancreatic thread protein"""	167770	"""regenerating islet-derived 1 alpha (pancreatic stone protein, pancreatic thread protein)"""	REG		2332435, 8333731	Standard	NM_002909		Approved	PSP, PTP, PSPS, PSPS1	uc002snz.3	P05451	OTTHUMG00000130016	ENST00000233735.1:c.444A>G	2.37:g.79350284A>G			P11379|Q4ZG28	Silent	SNP	pfam_C-type_lectin,superfamily_C-type_lectin_fold,smart_C-type_lectin,pfscan_C-type_lectin,prints_Pancreatis_ac,prints_AntifreezeII	p.K148	ENST00000233735.1	37	c.444	CCDS1964.1	2																																																																																			REG1A	-	pfam_C-type_lectin,superfamily_C-type_lectin_fold,smart_C-type_lectin,pfscan_C-type_lectin,prints_Pancreatis_ac	ENSG00000115386		0.423	REG1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	REG1A	HGNC	protein_coding	OTTHUMT00000252289.1	106	0.00	0	A	NM_002909		79350284	79350284	+1	no_errors	ENST00000233735	ensembl	human	known	69_37n	silent	90	41.18	63	SNP	0.082	G
RIOK2	55781	genome.wustl.edu	37	5	96506986	96506986	+	Missense_Mutation	SNP	T	T	C			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr5:96506986T>C	ENST00000283109.3	-	6	771	c.703A>G	c.(703-705)Att>Gtt	p.I235V	RIOK2_ENST00000508447.1_Missense_Mutation_p.I235V|CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	235							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.I235V(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		TCATCCAAAATGAGATTAAAT	0.348																																						dbGAP											2	Substitution - Missense(2)	breast(2)											84.0	80.0	81.0					5																	96506986		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.703A>G	5.37:g.96506986T>C	ENSP00000283109:p.Ile235Val		D6RDI3|Q9NUT0	Missense_Mutation	SNP	pfam_RIO-like_kinase,pfam_RIO2_kinase_winged_hlx_N,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,smart_RIO_kinase	p.I235V	ENST00000283109.3	37	c.703	CCDS4089.1	5	.	.	.	.	.	.	.	.	.	.	T	20.8	4.045343	0.75846	.	.	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.07327	3.2;3.2	5.17	5.17	0.71159	RIO kinase, conserved site (1);Protein kinase-like domain (1);RIO-like kinase (1);	0.092032	0.85682	D	0.000000	T	0.13114	0.0318	L	0.43598	1.365	0.46260	D	0.998956	B;B	0.30605	0.149;0.287	B;B	0.39935	0.299;0.314	T	0.04191	-1.0970	10	0.72032	D	0.01	-0.044	14.6673	0.68918	0.0:0.0:0.0:1.0	.	235;235	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	V	235	ENSP00000283109:I235V;ENSP00000420932:I235V	ENSP00000283109:I235V	I	-	1	0	RIOK2	96532742	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.032000	0.49736	1.957000	0.56846	0.482000	0.46254	ATT	RIOK2	-	pfam_RIO-like_kinase,pfam_LipoPS_kinase,superfamily_Kinase-like_dom,smart_RIO_kinase	ENSG00000058729		0.348	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RIOK2	HGNC	protein_coding	OTTHUMT00000250628.1	115	0.00	0	T	NM_018343		96506986	96506986	-1	no_errors	ENST00000283109	ensembl	human	known	69_37n	missense	81	39.55	53	SNP	1.000	C
SORCS1	114815	genome.wustl.edu	37	10	108427518	108427518	+	Silent	SNP	C	C	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr10:108427518C>T	ENST00000263054.6	-	17	2239	c.2232G>A	c.(2230-2232)ccG>ccA	p.P744P	SORCS1_ENST00000344440.6_Silent_p.P744P|SORCS1_ENST00000369698.1_Silent_p.P279P	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	744					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.P744P(2)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		ACCAAAATGCCGGCAGGCACT	0.463																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											74.0	67.0	69.0					10																	108427518		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2232G>A	10.37:g.108427518C>T			A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	pfam_PKD_dom,superfamily_PKD_dom,smart_VPS10,pfscan_PKD_dom	p.P744	ENST00000263054.6	37	c.2232	CCDS7559.1	10																																																																																			SORCS1	-	smart_VPS10	ENSG00000108018		0.463	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SORCS1	HGNC	protein_coding	OTTHUMT00000050232.4	37	0.00	0	C	NM_052918		108427518	108427518	-1	no_errors	ENST00000344440	ensembl	human	known	69_37n	silent	68	27.66	26	SNP	0.008	T
TIMM21	29090	genome.wustl.edu	37	18	71816295	71816296	+	Frame_Shift_Del	DEL	TG	TG	-	rs370815819		TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	TG	TG					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr18:71816295_71816296delTG	ENST00000169551.6	+	1	550_551	c.252_253delTG	c.(250-255)tctgtgfs	p.V85fs	FBXO15_ENST00000419743.2_5'Flank|TIMM21_ENST00000580087.1_Frame_Shift_Del_p.V85fs|FBXO15_ENST00000269500.5_5'Flank	NM_014177.2	NP_054896.2	Q9BVV7	TIM21_HUMAN	translocase of inner mitochondrial membrane 21 homolog (yeast)	85					cellular protein metabolic process (GO:0044267)|mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|protein import into mitochondrial matrix (GO:0030150)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane presequence translocase complex (GO:0005744)		p.V85fs*54(1)									AACAAGTGTCTGTGCACAGGAG	0.51																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			BC000892	CCDS12003.1	18q22.3	2011-11-25	2011-11-25	2011-11-25	ENSG00000075336	ENSG00000075336			25010	protein-coding gene	gene with protein product		615180	"""chromosome 18 open reading frame 55"""	C18orf55		11042152	Standard	NM_014177		Approved	HSPC154, TIM21	uc010dqr.1	Q9BVV7	OTTHUMG00000132844	ENST00000169551.6:c.252_253delTG	18.37:g.71816297_71816298delTG	ENSP00000169551:p.Val85fs		Q9P010	Frame_Shift_Del	DEL	pfam_Tim21	p.V85fs	ENST00000169551.6	37	c.252_253	CCDS12003.1	18																																																																																			TIMM21	-	NULL	ENSG00000075336		0.510	TIMM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TIMM21	HGNC	protein_coding	OTTHUMT00000256318.1	20	0.00	0	TG	NM_014177		71816295	71816296	+1	no_errors	ENST00000169551	ensembl	human	known	69_37n	frame_shift_del	46	24.59	15	DEL	0.482:0.558	-
TMEM218	219854	genome.wustl.edu	37	11	124967604	124967604	+	Silent	SNP	G	G	A			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr11:124967604G>A	ENST00000279968.4	-	5	569	c.246C>T	c.(244-246)gtC>gtT	p.V82V	TMEM218_ENST00000455225.1_Silent_p.V82V|TMEM218_ENST00000529583.1_Silent_p.V82V|TMEM218_ENST00000526175.1_Silent_p.V82V|TMEM218_ENST00000527766.1_Silent_p.V82V|TMEM218_ENST00000528724.1_Silent_p.V108V|TMEM218_ENST00000531909.1_Silent_p.V82V|TMEM218_ENST00000532407.1_Silent_p.V82V|TMEM218_ENST00000531262.1_5'UTR|TMEM218_ENST00000529609.1_3'UTR|TMEM218_ENST00000532156.1_3'UTR|TMEM218_ENST00000527271.1_Silent_p.V82V			A2RU14	TM218_HUMAN	transmembrane protein 218	82						integral component of membrane (GO:0016021)		p.V82V(1)		breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						AAGCCAGCAGGACATAGCGGC	0.448																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											90.0	75.0	80.0					11																	124967604		2201	4299	6500	-	-	-	SO:0001819	synonymous_variant	0				CCDS31715.1	11q24.2	2008-08-08			ENSG00000150433	ENSG00000150433			27344	protein-coding gene	gene with protein product							Standard	NM_001258238		Approved		uc031qeu.1	A2RU14		ENST00000279968.4:c.246C>T	11.37:g.124967604G>A			B7ZM48	Silent	SNP	NULL	p.V82	ENST00000279968.4	37	c.246	CCDS31715.1	11																																																																																			TMEM218	-	NULL	ENSG00000150433		0.448	TMEM218-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	TMEM218	HGNC	protein_coding	OTTHUMT00000386849.1	39	0.00	0	G	NM_001080546		124967604	124967604	-1	no_errors	ENST00000455225	ensembl	human	known	69_37n	silent	20	74.03	57	SNP	1.000	A
TPR	7175	genome.wustl.edu	37	1	186304588	186304588	+	Missense_Mutation	SNP	C	C	G	rs369991503		TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr1:186304588C>G	ENST00000367478.4	-	34	5089	c.4793G>C	c.(4792-4794)cGc>cCc	p.R1598P		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1598					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.R1599P(1)|p.R1598P(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CGCAGTAATGCGAACATCCAA	0.418			T	NTRK1	papillary thyroid																																	dbGAP		Dom	yes		1	1q25	7175	translocated promoter region		E	2	Substitution - Missense(2)	breast(2)											173.0	154.0	160.0					1																	186304588		1878	4112	5990	-	-	-	SO:0001583	missense	0			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.4793G>C	1.37:g.186304588C>G	ENSP00000356448:p.Arg1598Pro		Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	pfam_TPR_MLP1_2,superfamily_Prefoldin,superfamily_tRNA-bd_arm	p.R1598P	ENST00000367478.4	37	c.4793	CCDS41446.1	1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808983	0.90707	.	.	ENSG00000047410	ENST00000367478	T	0.27402	1.67	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.60209	0.2251	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.63910	-0.6530	10	0.56958	D	0.05	.	18.9661	0.92697	0.0:1.0:0.0:0.0	.	1598	P12270	TPR_HUMAN	P	1598	ENSP00000356448:R1598P	ENSP00000356448:R1598P	R	-	2	0	TPR	184571211	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	7.168000	0.77570	2.545000	0.85829	0.650000	0.86243	CGC	TPR	-	superfamily_Prefoldin	ENSG00000047410		0.418	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TPR	HGNC	protein_coding	OTTHUMT00000086353.2	214	0.00	0	C	NM_003292		186304588	186304588	-1	no_errors	ENST00000367478	ensembl	human	known	69_37n	missense	176	32.05	83	SNP	1.000	G
ZNF486	90649	genome.wustl.edu	37	19	20308876	20308877	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	AA	AA					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr19:20308876_20308877delAA	ENST00000335117.8	+	4	1414_1415	c.1357_1358delAA	c.(1357-1359)aagfs	p.K453fs	CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	453					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K447fs*12(1)|p.K453fs*>11(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						TAATAAACATAAGAGAATTCAT	0.337																																						dbGAP											2	Deletion - Frameshift(2)	breast(2)																																								-	-	-	SO:0001589	frameshift_variant	0			BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.1357_1358delAA	19.37:g.20308876_20308877delAA	ENSP00000335042:p.Lys453fs		Q0VG00	Frame_Shift_Del	DEL	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.K453fs	ENST00000335117.8	37	c.1357_1358	CCDS46029.1	19																																																																																			ZNF486	-	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000256229		0.337	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF486	HGNC	protein_coding	OTTHUMT00000447843.2	114	0.00	0	AA	NM_052852		20308876	20308877	+1	no_errors	ENST00000335117	ensembl	human	known	69_37n	frame_shift_del	84	10.42	10	DEL	0.994:0.994	-
ZNF627	199692	genome.wustl.edu	37	19	11727643	11727643	+	Missense_Mutation	SNP	G	G	T			TCGA-A2-A0YF-01A-21D-A10G-09	TCGA-A2-A0YF-10A-01D-A10G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	11571107-fe70-4140-afff-f4792a4fd473	0cf57576-caf9-46f4-9500-c7d5f1579b51	g.chr19:11727643G>T	ENST00000361113.5	+	4	533	c.325G>T	c.(325-327)Gtt>Ttt	p.V109F	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	109					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V109F(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						GTGTGGAGAAGTTGGCATGGG	0.428																																					Melanoma(112;173 1614 10731 17751 23322)	dbGAP											1	Substitution - Missense(1)	breast(1)											155.0	156.0	156.0					19																	11727643		2129	4262	6391	-	-	-	SO:0001583	missense	0			AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"""Zinc fingers, C2H2-type"", ""-"""	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.325G>T	19.37:g.11727643G>T	ENSP00000354414:p.Val109Phe		O14846|Q4KMP9|Q6NT81|Q9BRG4	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.V109F	ENST00000361113.5	37	c.325	CCDS42502.1	19	.	.	.	.	.	.	.	.	.	.	g	11.54	1.667916	0.29604	.	.	ENSG00000198551	ENST00000361113	T	0.15603	2.41	1.32	-1.12	0.09808	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.16514	0.0397	L	0.37697	1.125	0.09310	N	1	P	0.49090	0.919	P	0.50231	0.635	T	0.14671	-1.0464	9	0.56958	D	0.05	.	4.021	0.09665	0.4681:0.0:0.5319:0.0	.	109	Q7L945	ZN627_HUMAN	F	109	ENSP00000354414:V109F	ENSP00000354414:V109F	V	+	1	0	ZNF627	11588643	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.270000	0.08584	-0.253000	0.09514	0.313000	0.20887	GTT	ZNF627	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000198551		0.428	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF627	HGNC	protein_coding	OTTHUMT00000458875.1	105	0.00	0	G	NM_145295		11727643	11727643	+1	no_errors	ENST00000361113	ensembl	human	known	69_37n	missense	128	39.05	82	SNP	0.003	T
