#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CAF	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
UHMK1	127933	genome.wustl.edu	37	1	162469895	162469895	+	Missense_Mutation	SNP	G	G	T			TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr1:162469895G>T	ENST00000489294.1	+	2	577	c.419G>T	c.(418-420)cGa>cTa	p.R140L	UHMK1_ENST00000538489.1_Missense_Mutation_p.R140L|UHMK1_ENST00000282169.8_3'UTR|UHMK1_ENST00000545294.1_Missense_Mutation_p.R66L	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	140	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CATTGTGCCCGAGATGTTTTG	0.463																																							0											0													190.0	164.0	173.0					1																	162469895		2203	4300	6503	SO:0001583	missense	0			BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"""RNA binding motif (RRM) containing"""	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.419G>T	1.37:g.162469895G>T	ENSP00000420270:p.Arg140Leu		A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_RRM_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_RRM_dom,pfscan_RRM_dom,pfscan_Prot_kinase_dom	p.R140L	ENST00000489294.1	37	c.419	CCDS1239.1	1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884024	0.91814	.	.	ENSG00000152332	ENST00000545294;ENST00000538489;ENST00000489294	T;T;T	0.19669	2.13;2.13;2.13	5.53	5.53	0.82687	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.18383	0.0441	N	0.17901	0.54	.	.	.	D;D;D	0.69078	0.996;0.997;0.996	D;D;D	0.79784	0.988;0.993;0.988	T	0.05370	-1.0889	9	0.12430	T	0.62	-8.3027	16.5466	0.84448	0.0:0.0:1.0:0.0	.	140;140;66	Q8TAS1-2;Q8TAS1;G3V1M1	.;UHMK1_HUMAN;.	L	66;140;140	ENSP00000441226:R66L;ENSP00000446416:R140L;ENSP00000420270:R140L	ENSP00000420270:R140L	R	+	2	0	UHMK1	160736519	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.887000	0.92456	2.749000	0.94314	0.655000	0.94253	CGA	0	pfam_Prot_kinase_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_dom		0.463	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UHMK1	protein_coding	OTTHUMT00000076788.1	80	313	0	0.00	0	0	G	NM_175866	0	0		162469895	1	no_errors	ENST00000489294	ensembl	human	known	74_37	missense	64	275	18.99	15.12	15	49	SNP	1	T
ANGPTL1	9068	genome.wustl.edu	37	1	178821913	178821913	+	Missense_Mutation	SNP	C	C	A	rs570797031		TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr1:178821913C>A	ENST00000234816.2	-	5	1640	c.1193G>T	c.(1192-1194)cGc>cTc	p.R398L	RALGPS2_ENST00000367635.3_Intron|ANGPTL1_ENST00000367629.1_Missense_Mutation_p.R398L|RALGPS2_ENST00000367634.2_Intron	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	398	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						AGTTCCCAGGCGCAGTCTATA	0.398																																							0											0													124.0	123.0	123.0					1																	178821913		2203	4300	6503	SO:0001583	missense	0			AF107253	CCDS1327.1	1q25.2	2013-02-06			ENSG00000116194	ENSG00000116194		"""Fibrinogen C domain containing"""	489	protein-coding gene	gene with protein product	"""angioarrestin"""	603874		ANGPT3		10025962, 9286704	Standard	NM_004673		Approved	ANG3, AngY, ARP1	uc001gma.3	O95841	OTTHUMG00000035075	ENST00000234816.2:c.1193G>T	1.37:g.178821913C>A	ENSP00000234816:p.Arg398Leu		Q5T5Z5	Missense_Mutation	SNP	pfam_Fibrinogen_a/b/g_C_dom,superfamily_Fibrinogen_a/b/g_C_dom,smart_Fibrinogen_a/b/g_C_dom	p.R398L	ENST00000234816.2	37	c.1193	CCDS1327.1	1	.	.	.	.	.	.	.	.	.	.	C	34	5.405698	0.96051	.	.	ENSG00000116194	ENST00000234816;ENST00000367629	T;T	0.76968	-1.06;-1.06	5.67	5.67	0.87782	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	D	0.87297	0.6142	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85251	0.1044	10	0.36615	T	0.2	.	19.3618	0.94442	0.0:1.0:0.0:0.0	.	398	O95841	ANGL1_HUMAN	L	398	ENSP00000234816:R398L;ENSP00000356601:R398L	ENSP00000234816:R398L	R	-	2	0	ANGPTL1	177088536	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.818000	0.86416	2.660000	0.90430	0.650000	0.86243	CGC	0	pfam_Fibrinogen_a/b/g_C_dom,superfamily_Fibrinogen_a/b/g_C_dom,smart_Fibrinogen_a/b/g_C_dom		0.398	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANGPTL1	protein_coding	OTTHUMT00000084924.1	53	379	0	0.52	0	2	C	NM_004673	0	0		178821913	-1	no_errors	ENST00000234816	ensembl	human	known	74_37	missense	67	311	16.25	5.47	13	18	SNP	1	A
CD46	4179	genome.wustl.edu	37	1	207941138	207941138	+	Missense_Mutation	SNP	A	A	G			TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr1:207941138A>G	ENST00000358170.2	+	8	1072	c.916A>G	c.(916-918)Act>Gct	p.T306A	CD46_ENST00000361067.1_Missense_Mutation_p.T306A|CD46_ENST00000441839.2_Missense_Mutation_p.T291A|CD46_ENST00000469535.1_3'UTR|CD46_ENST00000357714.1_Intron|CD46_ENST00000322875.4_Missense_Mutation_p.T306A|CD46_ENST00000367041.1_Intron|CD46_ENST00000367042.1_Missense_Mutation_p.T291A|CD46_ENST00000480003.1_Missense_Mutation_p.T291A|CD46_ENST00000354848.1_Missense_Mutation_p.T291A|CD46_ENST00000367047.1_Missense_Mutation_p.T243A|CD46_ENST00000322918.5_Intron|CD46_ENST00000360212.2_Intron	NM_002389.4	NP_002380.3	P15529	MCP_HUMAN	CD46 molecule, complement regulatory protein	306	Ser/Thr-rich.				adaptive immune response (GO:0002250)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|interleukin-10 production (GO:0032613)|negative regulation of complement activation (GO:0045916)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transforming growth factor beta production (GO:0071636)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)|regulation of Notch signaling pathway (GO:0008593)|sequestering of extracellular ligand from receptor (GO:0035581)|single fertilization (GO:0007338)|T cell mediated immunity (GO:0002456)|viral process (GO:0016032)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|inner acrosomal membrane (GO:0002079)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cadherin binding (GO:0045296)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	19						GACTTCTTCCACTACAAAATC	0.348																																							0											0													113.0	114.0	114.0					1																	207941138		2203	4300	6503	SO:0001583	missense	0			BC030594	CCDS1479.1, CCDS1480.1, CCDS1481.1, CCDS1482.1, CCDS1484.1, CCDS1485.1, CCDS31008.1, CCDS31009.1	1q32	2014-09-17	2006-03-28	2006-02-09	ENSG00000117335	ENSG00000117335		"""CD molecules"", ""Complement system"""	6953	protein-coding gene	gene with protein product		120920	"""antigen identified by monoclonal antibody TRA-2-10"", ""membrane cofactor protein (CD46, trophoblast-lymphocyte cross-reactive antigen)"", ""CD46 antigen, complement regulatory protein"""	MIC10, MCP		7929741	Standard	NM_002389		Approved	TRA2.10, MGC26544, TLX	uc001hgj.3	P15529	OTTHUMG00000036397	ENST00000358170.2:c.916A>G	1.37:g.207941138A>G	ENSP00000350893:p.Thr306Ala		A0T1T0|A0T1T1|A0T1T2|Q15429|Q53GV9|Q5HY94|Q5VWS6|Q5VWS7|Q5VWS8|Q5VWS9|Q5VWT0|Q5VWT1|Q5VWT2|Q6N0A1|Q7Z3R5|Q9NNW2|Q9NNW3|Q9NNW4|Q9UCJ4	Missense_Mutation	SNP	pirsf_M_CF_CD46,pfam_Sushi_SCR_CCP,superfamily_Sushi_SCR_CCP,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP	p.T306A	ENST00000358170.2	37	c.916	CCDS1485.1	1	.	.	.	.	.	.	.	.	.	.	A	8.657	0.899619	0.17686	.	.	ENSG00000117335	ENST00000358170;ENST00000354848;ENST00000367042;ENST00000322875;ENST00000367047;ENST00000441839;ENST00000361067;ENST00000480003	T;T;T;T;T;T;T;T	0.44083	1.29;1.3;1.22;1.3;1.25;1.23;0.93;0.93	4.1	2.94	0.34122	.	.	.	.	.	T	0.22205	0.0535	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B;B;B;B	0.28850	0.225;0.225;0.225;0.225;0.225;0.225;0.225;0.225;0.144	B;B;B;B;B;B;B;B;B	0.33042	0.157;0.11;0.157;0.11;0.157;0.11;0.157;0.11;0.051	T	0.25433	-1.0132	9	0.21540	T	0.41	.	6.7974	0.23732	0.7926:0.0:0.0:0.2074	.	306;291;291;306;306;291;291;291;306	P15529-5;P15529-14;P15529-3;P15529-13;P15529-2;P15529-11;P15529-6;P15529-8;P15529	.;.;.;.;.;.;.;.;MCP_HUMAN	A	306;291;291;306;243;291;306;291	ENSP00000350893:T306A;ENSP00000346912:T291A;ENSP00000356009:T291A;ENSP00000313875:T306A;ENSP00000356014:T243A;ENSP00000413543:T291A;ENSP00000354358:T306A;ENSP00000418471:T291A	ENSP00000313875:T306A	T	+	1	0	CD46	206007761	0.005000	0.15991	0.122000	0.21767	0.017000	0.09413	0.979000	0.29500	0.858000	0.35431	0.533000	0.62120	ACT	0	pirsf_M_CF_CD46		0.348	CD46-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CD46	protein_coding	OTTHUMT00000088588.3	82	451	1.2	0.00	1	0	A	NM_172361	0	0		207941138	1	no_errors	ENST00000322875	ensembl	human	known	74_37	missense	88	440	7.37	5.17	7	24	SNP	0.182	G
OR2T1	26696	genome.wustl.edu	37	1	248569756	248569756	+	Missense_Mutation	SNP	A	A	G			TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr1:248569756A>G	ENST00000366474.1	+	1	461	c.461A>G	c.(460-462)tAc>tGc	p.Y154C		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(24)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	39	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACTTCCTCTACCTTACCCTT	0.488																																							0											0													163.0	158.0	159.0					1																	248569756		2203	4300	6503	SO:0001583	missense	0			U86215	CCDS31115.1	1q44	2012-08-09			ENSG00000175143	ENSG00000175143		"""GPCR / Class A : Olfactory receptors"""	8277	protein-coding gene	gene with protein product						9500546	Standard	NM_030904		Approved	OR1-25	uc010pzm.2	O43869	OTTHUMG00000040450	ENST00000366474.1:c.461A>G	1.37:g.248569756A>G	ENSP00000355430:p.Tyr154Cys		Q6IEZ9	Missense_Mutation	SNP	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.Y154C	ENST00000366474.1	37	c.461	CCDS31115.1	1	.	.	.	.	.	.	.	.	.	.	a	15.01	2.705929	0.48412	.	.	ENSG00000175143	ENST00000366474	T	0.00542	6.69	4.75	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33553	U	0.004799	T	0.00580	0.0019	L	0.35249	1.045	0.26552	N	0.973886	P	0.41475	0.751	B	0.42738	0.396	T	0.54820	-0.8236	10	0.62326	D	0.03	.	10.0014	0.41931	0.8492:0.0:0.0:0.1508	.	154	O43869	OR2T1_HUMAN	C	154	ENSP00000355430:Y154C	ENSP00000355430:Y154C	Y	+	2	0	OR2T1	246636379	0.117000	0.22190	0.908000	0.35775	0.909000	0.53808	2.248000	0.43160	1.993000	0.58246	0.528000	0.53228	TAC	0	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_GPCR_Rhodpsn		0.488	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR2T1	protein_coding	OTTHUMT00000097346.2	40	254	0	0.39	0	1	A		0	0		248569756	1	no_errors	ENST00000366474	ensembl	human	known	74_37	missense	50	193	24.24	22.18	16	55	SNP	0.475	G
MTX3	345778	genome.wustl.edu	37	5	79284999	79284999	+	Silent	SNP	G	G	T			TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr5:79284999G>T	ENST00000512528.1	-	4	317	c.297C>A	c.(295-297)ctC>ctA	p.L99L	MTX3_ENST00000512560.1_Silent_p.L38L|MTX3_ENST00000509852.1_Silent_p.L99L			Q5HYI7	MTX3_HUMAN	metaxin 3	99					protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				endometrium(1)|large_intestine(3)|lung(2)|urinary_tract(1)	7		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.63e-45)|Epithelial(54;2.9e-40)|all cancers(79;4.68e-35)		GCTTCTCTTCGAGGAGAGCAA	0.338																																							0											0													56.0	54.0	54.0					5																	79284999		1831	4091	5922	SO:0001819	synonymous_variant	0			BX538064	CCDS47239.1, CCDS47239.2, CCDS54872.1	5q14.1	2004-08-18				ENSG00000177034			24812	protein-coding gene	gene with protein product						15087125	Standard	NM_001010891		Approved		uc010jah.3	Q5HYI7		ENST00000512528.1:c.297C>A	5.37:g.79284999G>T			B4DL65|E9PB57|Q7Z380|Q8NB92	Silent	SNP	pfam_Sam37/metaxin,superfamily_Glutathione-S-Trfase_C-like,pirsf_Metaxin	p.L99	ENST00000512528.1	37	c.297		5																																																																																			0	pfam_Sam37/metaxin,pirsf_Metaxin		0.338	MTX3-005	KNOWN	basic|appris_principal	protein_coding	MTX3	protein_coding	OTTHUMT00000372567.1	170	241	0	0.82	0	2	G	XM_293971	0	0		79284999	-1	no_errors	ENST00000512528	ensembl	human	known	74_37	silent	147	244	9.26	7.55	15	20	SNP	0.004	T
SHC4	399694	genome.wustl.edu	37	15	49170368	49170368	+	Intron	SNP	T	T	C			TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr15:49170368T>C	ENST00000332408.4	-	5	1269				EID1_ENST00000530028.2_5'UTR|EID1_ENST00000560490.1_5'UTR|SHC4_ENST00000537958.1_5'Flank|EID1_ENST00000558295.1_3'UTR|SHC4_ENST00000396535.3_5'Flank	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4						apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		TTGAGCGGTTTGCACAATGTC	0.587																																							0											0													95.0	99.0	98.0					15																	49170368		2089	4231	6320	SO:0001627	intron_variant	0			AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"""SH2 domain containing"""	16743	protein-coding gene	gene with protein product	"""rai-like protein"""						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.841-6029A>G	15.37:g.49170368T>C			Q6UXQ3|Q8IYW3	RNA	SNP	0	NULL	ENST00000332408.4	37	NULL	CCDS10130.1	15																																																																																			0	0		0.587	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EID1	protein_coding	OTTHUMT00000254371.1	44	219	0	0.00	0	0	T	NM_203349	0	0		49170368	1	no_errors	ENST00000558295	ensembl	human	putative	74_37	rna	34	161	17.07	11.48	7	21	SNP	0	C
CFDP1	10428	genome.wustl.edu	37	16	75428996	75428996	+	Silent	SNP	G	G	A	rs371488344		TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr16:75428996G>A	ENST00000283882.3	-	5	774	c.642C>T	c.(640-642)gcC>gcT	p.A214A		NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	214	Hydrophilic.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						ACCCTGACCCGGCAGGGAGTG	0.473													G|||	1	0.000199681	0.0	0.0	5008	,	,		18446	0.0		0.0	False		,,,				2504	0.001						0.9998,0.0001997											0								G		0,4396		0,0,2198	118.0	113.0	115.0		642	-8.1	0.5	16		115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CFDP1	NM_006324.2		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		214/300	75428996	1,12995	2198	4300	6498	SO:0001819	synonymous_variant	0			AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774			1873	protein-coding gene	gene with protein product	"""Bucentaur"", ""centromere protein 29"""	608108				9602175, 9006920, 11992732	Standard	NM_006324		Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.642C>T	16.37:g.75428996G>A			O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	Silent	SNP	pfam_BCNT-C	p.A214	ENST00000283882.3	37	c.642	CCDS10916.1	16																																																																																			0	NULL		0.473	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CFDP1	protein_coding	OTTHUMT00000269031.2	65	259	0	0.00	0	0	G	NM_006324	rs371488344	G->A		75428996	-1	no_errors	ENST00000283882	ensembl	human	known	74_37	silent	52	180	7.14	5.26	4	10	SNP	0.722	A
SYN3	8224	genome.wustl.edu	37	22	32923933	32923933	+	Silent	SNP	G	G	A			TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr22:32923933G>A	ENST00000358763.2	-	12	1532	c.1290C>T	c.(1288-1290)ggC>ggT	p.G430G	SYN3_ENST00000332840.5_Silent_p.G430G	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	430	J; Pro-rich linker.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						GCTGGGGCTGGCCTAGCTGAG	0.577																																							0											0													26.0	24.0	25.0					22																	32923933		2202	4298	6500	SO:0001819	synonymous_variant	0			AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.1290C>T	22.37:g.32923933G>A			B1B1F9	Silent	SNP	pfam_Synapsin_ATP-bd_dom,pfam_Synapsin_pre-ATP-grasp_dom,pfam_Synapsin_P_site,pfam_ATP-grasp_RimK-type,superfamily_PreATP-grasp_dom,prints_Synapsin	p.G430	ENST00000358763.2	37	c.1290	CCDS13908.1	22																																																																																			0	NULL		0.577	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SYN3	protein_coding	OTTHUMT00000075892.4	77	73	0	0.00	0	0	G		0	0		32923933	-1	no_errors	ENST00000332840	ensembl	human	known	74_37	silent	62	70	7.35	4.11	5	3	SNP	1	A
EP400NL	347918	genome.wustl.edu	37	12	132589423	132589423	+	Silent	SNP	G	G	A	rs374559184		TCGA-4V-A9QS-01A-11D-A423-09	TCGA-4V-A9QS-10A-01D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	2a777225-39dc-48da-b630-ae004006f6db	17622cfb-dcdf-43b3-b287-3beaca4b2980	g.chr12:132589423G>A	ENST00000376625.4	+	1	884	c.858G>A	c.(856-858)acG>acA	p.T286T	EP400NL_ENST00000392352.1_Silent_p.T154T|EP400NL_ENST00000443539.2_Silent_p.T154T|EP400NL_ENST00000361109.5_Silent_p.T133T|EP400NL_ENST00000389560.2_Silent_p.T217T			Q6ZTU2	E400N_HUMAN	EP400 N-terminal like	286										endometrium(1)|lung(1)|prostate(2)|urinary_tract(1)	5						TCGAGAGGACGCCCGGCGTGC	0.741																																							0											0													9.0	12.0	11.0					12																	132589423		686	1581	2267	SO:0001819	synonymous_variant	0			AK091234		12q24.33	2013-02-15			ENSG00000185684	ENSG00000185684			26602	protein-coding gene	gene with protein product						12477932	Standard	NR_003290		Approved	FLJ33915	uc009zyq.3	Q6ZTU2	OTTHUMG00000168251	ENST00000376625.4:c.858G>A	12.37:g.132589423G>A			A6NLB7|A8K0Z5|B3KQY2|Q6NXP1|Q8N253|Q8N7S7|Q9UFJ3	Silent	SNP	NULL	p.T286	ENST00000376625.4	37	c.858		12																																																																																			0	NULL		0.741	EP400NL-202	KNOWN	basic|appris_candidate_longest	protein_coding	EP400NL	protein_coding		10	12	0	0.00	0	0	G	NM_182613	rs374559184	G->A		132589423	1	no_errors	ENST00000376625	ensembl	human	known	74_37	silent	14	7	17.65	0.00	3	0	SNP	0.189	A
