#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
MOCS1	4337	broad.mit.edu	37	6	39893572	39893572	+	Missense_Mutation	SNP	C	C	G	rs147580725		TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr6:39893572C>G	ENST00000340692.5	-	3	271	c.268G>C	c.(268-270)Gag>Cag	p.E90Q	MOCS1_ENST00000308559.7_Missense_Mutation_p.E90Q|MOCS1_ENST00000373175.4_Missense_Mutation_p.E61Q|MOCS1_ENST00000432280.2_Missense_Mutation_p.E61Q|MOCS1_ENST00000373186.4_Missense_Mutation_p.E90Q|MOCS1_ENST00000373188.2_Missense_Mutation_p.E90Q|MOCS1_ENST00000373195.3_Missense_Mutation_p.E3Q|MOCS1_ENST00000425303.2_Missense_Mutation_p.E90Q			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	90	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					ACCCCCTCCTCGGGCATGCAG	0.612																																					NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	ENST00000373186.4																			0				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21						c.(268-270)Gag>Cag		molybdenum cofactor synthesis 1							45.0	52.0	49.0					6																	39893572		2201	4290	6491	SO:0001583	missense	4337				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding	g.chr6:39893572C>G	AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.268G>C	6.37:g.39893572C>G	ENSP00000344794:p.Glu90Gln					MOCS1_ENST00000432280.2_Missense_Mutation_p.E61Q|MOCS1_ENST00000373175.4_Missense_Mutation_p.E61Q|MOCS1_ENST00000373195.3_Missense_Mutation_p.E3Q|MOCS1_ENST00000425303.2_Missense_Mutation_p.E90Q|MOCS1_ENST00000373188.2_Missense_Mutation_p.E90Q|MOCS1_ENST00000308559.7_Missense_Mutation_p.E90Q|MOCS1_ENST00000340692.5_Missense_Mutation_p.E90Q	p.E90Q	NM_005943.5	NP_005934.2	Q9NZB8	MOCS1_HUMAN			2	405	-	Ovarian(28;0.0355)|Colorectal(47;0.196)		90			Molybdenum cofactor biosynthesis protein A.		B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	37	c.268G>C		.	.	.	.	.	.	.	.	.	.	C	22.1	4.244478	0.79912	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T;T;T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34;1.34;-1.34;-1.34;-1.34	5.08	5.08	0.68730	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);Radical SAM (1);	0.107097	0.64402	D	0.000007	D	0.83894	0.5353	M	0.81614	2.55	0.31466	N	0.66895	P;B;P;B;B	0.39737	0.635;0.334;0.685;0.406;0.243	P;B;P;B;B	0.50490	0.565;0.307;0.642;0.387;0.38	T	0.82729	-0.0313	9	.	.	.	-21.0518	18.4896	0.90842	0.0:1.0:0.0:0.0	.	90;90;90;90;90	Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;.;MOCS1_HUMAN;.;.	Q	90;90;61;90;3;90;90;61	ENSP00000362282:E90Q;ENSP00000309843:E90Q;ENSP00000362270:E61Q;ENSP00000362284:E90Q;ENSP00000362291:E3Q;ENSP00000344794:E90Q;ENSP00000416478:E90Q;ENSP00000410809:E61Q	.	E	-	1	0	MOCS1	40001550	1.000000	0.71417	0.990000	0.47175	0.933000	0.57130	5.672000	0.68102	2.538000	0.85594	0.485000	0.47835	GAG		0.612	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943		3	94	0	0	0	0.004672	0	3	94				
IGHV1OR16-3	28313	broad.mit.edu	37	16	32070612	32070612	+	RNA	SNP	A	A	C	rs368458790		TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr16:32070612A>C	ENST00000566806.1	-	0	499																											GGTCTCCTGCAAGGCTTCTGG	0.552																																						ENST00000566806.1																			0																																																			0							g.chr16:32070612A>C																													16.37:g.32070612A>C														0	499	-									RNA	SNP	ENST00000566806.1	37																																																																																						0.552	RP11-1166P10.6-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432459.1			4	38	0	0	0	0.014758	0	4	38				
LRP1	4035	broad.mit.edu	37	12	57577587	57577587	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr12:57577587G>T	ENST00000243077.3	+	36	6290	c.5824G>T	c.(5824-5826)Ggc>Tgc	p.G1942C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1942					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GGTGGACATGGGCCTGAGCAC	0.577																																						ENST00000243077.3																			0				NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184						c.(5824-5826)Ggc>Tgc		low density lipoprotein receptor-related protein 1	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)						82.0	73.0	76.0					12																	57577587		2203	4300	6503	SO:0001583	missense	4035				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity	g.chr12:57577587G>T	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.5824G>T	12.37:g.57577587G>T	ENSP00000243077:p.Gly1942Cys						p.G1942C	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0103)	36	6290	+			1942					Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	c.5824G>T	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.807058	0.90623	.	.	ENSG00000123384	ENST00000243077	D	0.91843	-2.92	5.47	5.47	0.80525	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000002	D	0.96346	0.8808	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96571	0.9423	10	0.66056	D	0.02	.	18.0915	0.89477	0.0:0.0:1.0:0.0	.	1942	Q07954	LRP1_HUMAN	C	1942	ENSP00000243077:G1942C	ENSP00000243077:G1942C	G	+	1	0	LRP1	55863854	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.580000	0.87095	0.561000	0.74099	GGC		0.577	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		4	62	1	0	0.00024832	0.009096	0.00148992	4	62				
YY1	7528	broad.mit.edu	37	14	100743846	100743846	+	Missense_Mutation	SNP	G	G	T			TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr14:100743846G>T	ENST00000262238.4	+	5	1414	c.1154G>T	c.(1153-1155)tGc>tTc	p.C385F	AL157871.2_ENST00000553954.1_RNA	NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN	YY1 transcription factor	385	Binding to DNA.|Involved in masking transactivation domain.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|cell differentiation (GO:0030154)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromosome organization (GO:0051276)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to prostaglandin F (GO:0034696)|response to UV-C (GO:0010225)|RNA localization (GO:0006403)|spermatogenesis (GO:0007283)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|four-way junction DNA binding (GO:0000400)|RNA binding (GO:0003723)|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 transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.C385F(1)		cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11		Melanoma(154;0.152)				CCCTATGTGTGCCCCTTCGAT	0.463																																						ENST00000262238.4																			1	Substitution - Missense(1)	p.C385F(1)	lung(1)	cervix(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)|prostate(4)|skin(1)	11						c.(1153-1155)tGc>tTc		YY1 transcription factor							115.0	103.0	107.0					14																	100743846		2203	4300	6503	SO:0001583	missense	7528				cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding	g.chr14:100743846G>T	BC020324	CCDS9957.1	14q	2013-01-08			ENSG00000100811	ENSG00000100811		"""INO80 complex subunits"", ""Zinc fingers, C2H2-type"""	12856	protein-coding gene	gene with protein product	"""INO80 complex subunit S"", ""Yin and Yang 1 protein"""	600013				1655281, 7912122	Standard	NM_003403		Approved	NF-E1, DELTA, UCRBP, YIN-YANG-1, INO80S	uc001ygy.2	P25490	OTTHUMG00000150479	ENST00000262238.4:c.1154G>T	14.37:g.100743846G>T	ENSP00000262238:p.Cys385Phe						p.C385F	NM_003403.3	NP_003394.1	P25490	TYY1_HUMAN			5	1414	+		Melanoma(154;0.152)	385			Involved in masking transactivation domain.		Q14935	Missense_Mutation	SNP	ENST00000262238.4	37	c.1154G>T	CCDS9957.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.40|19.40	3.819772|3.819772	0.71028|0.71028	.|.	.|.	ENSG00000100811|ENSG00000100811	ENST00000554804|ENST00000262238	.|D	.|0.85088	.|-1.94	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.85682	.|U	.|0.000000	D|D	0.95001|0.95001	0.8382|0.8382	H|H	0.94423|0.94423	3.535|3.535	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.95618|0.95618	0.8678|0.8678	5|10	.|0.87932	.|D	.|0	.|.	20.0965|20.0965	0.97849|0.97849	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|385	.|P25490	.|TYY1_HUMAN	S|F	161|385	.|ENSP00000262238:C385F	.|ENSP00000262238:C385F	A|C	+|+	1|2	0|0	YY1|YY1	99813599|99813599	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.779000|9.779000	0.99018|0.99018	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	GCC|TGC		0.463	YY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318277.1	NM_003403		7	69	1	0	2.7689e-08	0.029380	1.93823e-07	7	69				
NUTM2B-AS1	101060691	broad.mit.edu	37	10	81444997	81444997	+	RNA	SNP	T	T	C	rs370178959		TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr10:81444997T>C	ENST00000600376.1	-	0	54				RP11-119F19.2_ENST00000596088.1_RNA																							ACAACAATTTTCGGGCTTGCA	0.612																																						ENST00000600376.1																			0																																																			0							g.chr10:81444997T>C																													10.37:g.81444997T>C						RP11-119F19.2_ENST00000596088.1_RNA								0	54	-									RNA	SNP	ENST00000600376.1	37																																																																																						0.612	RP11-119F19.2-004	KNOWN	basic	antisense	antisense	OTTHUMT00000461766.1			2	4	0	0	0	0.004672	0	2	4				
LGI2	55203	broad.mit.edu	37	4	25005303	25005303	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr4:25005303A>G	ENST00000382114.4	-	8	1593	c.1408T>C	c.(1408-1410)Ttt>Ctt	p.F470L		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	470						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				TTAAAAGAAAAGGGCTGCAGG	0.488																																						ENST00000382114.4																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33						c.(1408-1410)Ttt>Ctt		leucine-rich repeat LGI family, member 2							99.0	112.0	108.0					4																	25005303		2203	4300	6503	SO:0001583	missense	55203					extracellular region		g.chr4:25005303A>G	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.1408T>C	4.37:g.25005303A>G	ENSP00000371548:p.Phe470Leu						p.F470L	NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN			8	1593	-		Breast(46;0.173)	470					Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Missense_Mutation	SNP	ENST00000382114.4	37	c.1408T>C	CCDS3431.1	.	.	.	.	.	.	.	.	.	.	A	6.520	0.464214	0.12402	.	.	ENSG00000153012	ENST00000382114;ENST00000282970	D	0.86497	-2.13	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.81024	0.4737	L	0.28649	0.875	0.80722	D	1	B	0.17852	0.024	B	0.26969	0.075	T	0.75286	-0.3371	10	0.11485	T	0.65	-20.267	16.0985	0.81148	1.0:0.0:0.0:0.0	.	470	Q8N0V4	LGI2_HUMAN	L	470;118	ENSP00000371548:F470L	ENSP00000282970:F118L	F	-	1	0	LGI2	24614401	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	2.197000	0.70478	0.455000	0.32223	TTT		0.488	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			3	137	0	0	0	0.004672	0	3	137				
HLA-V	352962	broad.mit.edu	37	6	29760353	29760373	+	RNA	DEL	GCGGGCGCCGTGGATGGAGCA	GCGGGCGCCGTGGATGGAGCA	-	rs60681449|rs2905755|rs140982245	byFrequency	TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr6:29760353_29760373delGCGGGCGCCGTGGATGGAGCA	ENST00000457107.1	+	0	223_243									major histocompatibility complex, class I, V (pseudogene)																		GGATGGAGCCGCGGGCGCCGTGGATGGAGCAGGAGGGGCCG	0.674																																						ENST00000457107.1																			0																																																			0							g.chr6:29760353_29760373delGCGGGCGCCGTGGATGGAGCA	M96332		6p21.3	2012-10-05	2007-12-12	2007-12-12	ENSG00000181126	ENSG00000181126		"""Histocompatibility complex"""	23482	pseudogene	pseudogene			"""HLA-75 pseudogene"""	HLA-75			Standard	NG_002729		Approved	dJ377H14.4			OTTHUMG00000031277		6.37:g.29760353_29760373delGCGGGCGCCGTGGATGGAGCA														0	223_243	+									RNA	DEL	ENST00000457107.1	37																																																																																						0.674	HLA-V-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000105231.1	NG_002729		4	9						4	9	---	---	---	---
CCT6P1	643253	broad.mit.edu	37	7	65226569	65226569	+	RNA	DEL	T	T	-			TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr7:65226569delT	ENST00000442266.1	+	0	1167				SNORA15_ENST00000384058.1_RNA					chaperonin containing TCP1, subunit 6 (zeta) pseudogene 1																		gcccggccCCttttttttttt	0.413																																						ENST00000442266.1																			0																																																			0							g.chr7:65226569delT	BC052238, BC073761		7q11.21	2010-06-29	2008-09-22	2008-09-22	ENSG00000228409	ENSG00000228409			33094	pseudogene	pseudogene			"""chaperonin containing TCP1, subunit 6A (zeta 1) pseudogene 1"""	CCT6AP1			Standard	NR_003110		Approved		uc003tug.3		OTTHUMG00000156733		7.37:g.65226569delT														0	1167	+									RNA	DEL	ENST00000442266.1	37																																																																																						0.413	CCT6P1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345507.1	NR_003110		2	4						2	4	---	---	---	---
KIZ-AS1	101929591	broad.mit.edu	37	20	21196192	21196192	+	RNA	DEL	T	T	-			TCGA-CS-6669-01A-11D-1893-08	TCGA-CS-6669-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	218a9531-9264-43bc-8535-858d4cb0919e	4bc99b08-8b67-443e-88a4-03edef39d433	g.chr20:21196192delT	ENST00000591761.1	-	0	119				RP4-777D9.2_ENST00000433213.2_RNA|PLK1S1_ENST00000457464.1_RNA|RP4-777D9.2_ENST00000443753.1_RNA																							TTTGAAATACTTTTTTTTTAT	0.323																																						ENST00000591761.1																			0																,,	29,3455		3,23,1716	27.0	27.0	27.0		,,	0.5	0.0	20		27	86,7720		7,72,3824	no	intron,intron,intron	PLK1S1	NM_018474.4,NM_001163023.1,NM_001163022.1	,,	10,95,5540	A1A1,A1R,RR		1.1017,0.8324,1.0186	,,	,,	21196192	115,11175	1804	4072	5876			0							g.chr20:21196192delT																													20.37:g.21196192delT						PLK1S1_ENST00000457464.1_RNA|RP4-777D9.2_ENST00000433213.2_RNA|RP4-777D9.2_ENST00000443753.1_RNA								0	119	-									RNA	DEL	ENST00000591761.1	37																																																																																						0.323	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2			2	4						2	4	---	---	---	---
