#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
LILRB1	10859	broad.mit.edu	37	19	55145098	55145098	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr19:55145098G>A	ENST00000396331.1	+	9	1628	c.1271G>A	c.(1270-1272)gGg>gAg	p.G424E	LILRB1_ENST00000324602.7_Missense_Mutation_p.G424E|LILRB1_ENST00000396332.4_Missense_Mutation_p.G424E|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Missense_Mutation_p.G424E|LILRB1_ENST00000434867.2_Missense_Mutation_p.G424E|LILRB1_ENST00000396327.3_Missense_Mutation_p.G424E|LILRB1_ENST00000396317.1_Intron|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000427581.2_Missense_Mutation_p.G460E|LILRB1_ENST00000396321.2_Missense_Mutation_p.G424E|LILRB1_ENST00000396315.1_Missense_Mutation_p.G424E	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	424					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		GGACCGTCTGGGGGCCCCAGC	0.612										HNSCC(37;0.09)																												uc002qgm.3																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74						c.(1270-1272)gGg>gAg		Homo sapiens leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1 (LILRB1), transcript variant 2, mRNA.							27.0	32.0	31.0					19																	55145098		1913	4118	6031	SO:0001583	missense	10859				regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity	g.chr19:55145098G>A	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1271G>A	19.37:g.55145098G>A	ENSP00000379622:p.Gly424Glu	HNSCC(37;0.09)	Somatic				LILRB1_uc010erp.1_Intron|LILRB1_uc002qgj.3_Missense_Mutation_p.G424E|LILRB1_uc002qgl.3_Missense_Mutation_p.G424E|LILRB1_uc002qgk.3_Missense_Mutation_p.G424E|LILRB1_uc010erq.3_Intron|LILRB1_uc010err.3_Non-coding_Transcript	p.G424E	NM_001081637	NP_001075106	WXS	Illumina GAIIx	Phase_I	Q8NHL6	LIRB1_HUMAN		GBM - Glioblastoma multiforme(193;0.0188)	7	1436	+			424					A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	c.1271G>A	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.438043	0.01098	.	.	ENSG00000104972	ENST00000396321;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396315	T;T;T;T;T;T;T;T;T	0.00505	7.07;6.93;7.07;7.05;7.03;7.07;7.07;7.06;7.03	2.02	-0.245	0.13027	.	.	.	.	.	T	0.00328	0.0010	L	0.39245	1.2	0.09310	N	1	B;B;B;B	0.16396	0.007;0.017;0.016;0.011	B;B;B;B	0.23852	0.02;0.027;0.049;0.016	T	0.45131	-0.9282	9	0.02654	T	1	.	4.1604	0.10280	0.3938:0.0:0.6062:0.0	.	424;424;424;424	Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;LIRB1_HUMAN	E	424;424;424;424;424;424;424;460;424	ENSP00000379614:G424E;ENSP00000409968:G424E;ENSP00000379622:G424E;ENSP00000379618:G424E;ENSP00000315997:G424E;ENSP00000405243:G424E;ENSP00000379623:G424E;ENSP00000395004:G460E;ENSP00000379608:G424E	ENSP00000315997:G424E	G	+	2	0	LILRB1	59836910	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.050000	0.14120	0.013000	0.14918	0.195000	0.17529	GGG		0.612	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			13	8	0	0	0	1	0	13	8				
SMARCD3	6604	broad.mit.edu	37	7	150936733	150936733	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr7:150936733G>A	ENST00000262188.8	-	11	1683	c.1273C>T	c.(1273-1275)Cgc>Tgc	p.R425C	MIR671_ENST00000390183.1_RNA|SMARCD3_ENST00000356800.2_Missense_Mutation_p.R412C|SMARCD3_ENST00000392811.2_Missense_Mutation_p.R412C|RP4-548D19.3_ENST00000607902.1_RNA|SMARCD3_ENST00000477169.1_5'Flank	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	425					cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTCTGGGAGCGGAGCAGGTCT	0.537																																						uc003wjs.3																			0				haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15						c.(1273-1275)Cgc>Tgc		Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3 (SMARCD3), transcript variant 3, mRNA.							108.0	111.0	110.0					7																	150936733		2203	4300	6503	SO:0001583	missense	6604				cellular lipid metabolic process|chromatin modification|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	SWI/SNF complex|nBAF complex|npBAF complex|nucleoplasm	nuclear hormone receptor binding|protein binding|transcription coactivator activity|transcription factor binding	g.chr7:150936733G>A	U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60C"", ""Swp73-like protein"", ""SWI/SNF complex 60 kDa subunit C"", ""60kDa BRG-1/Brm associated factor subunit c"""	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.1273C>T	7.37:g.150936733G>A	ENSP00000262188:p.Arg425Cys		Somatic				SMARCD3_uc003wjt.3_Missense_Mutation_p.R412C|SMARCD3_uc003wju.3_Missense_Mutation_p.R412C	p.R425C	NM_001003801	NP_001003801	WXS	Illumina GAIIx	Phase_I	Q6STE5	SMRD3_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	10	1374	-			425					D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Missense_Mutation	SNP	ENST00000262188.8	37	c.1273C>T	CCDS34780.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.364043	0.41902	.	.	ENSG00000082014	ENST00000262188;ENST00000392811;ENST00000356800;ENST00000347683	T;T;T	0.44482	0.92;0.92;0.92	5.09	4.21	0.49690	.	0.267477	0.39687	N	0.001296	T	0.26702	0.0653	N	0.14661	0.345	0.49582	D	0.999804	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.05484	-1.0882	10	0.56958	D	0.05	-5.6327	11.3474	0.49569	0.0888:0.0:0.9112:0.0	.	412;425	Q6STE5-2;Q6STE5	.;SMRD3_HUMAN	C	425;412;412;377	ENSP00000262188:R425C;ENSP00000376558:R412C;ENSP00000349254:R412C	ENSP00000262188:R425C	R	-	1	0	SMARCD3	150567666	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.304000	0.43655	1.148000	0.42385	0.655000	0.94253	CGC		0.537	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801		15	112	0	0	0	1	0	15	112				
SNX9	51429	broad.mit.edu	37	6	158342658	158342658	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr6:158342658G>A	ENST00000392185.3	+	10	1216	c.1045G>A	c.(1045-1047)Gtt>Att	p.V349I		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	349	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		AGAAAGTGAAGTTTTCCAGCA	0.428																																						uc003qqv.1																			0		p.E348*(2)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20						c.(1045-1047)Gtt>Att		Homo sapiens sorting nexin 9 (SNX9), mRNA.							85.0	81.0	83.0					6																	158342658		2203	4300	6503	SO:0001583	missense	51429				cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding	g.chr6:158342658G>A	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"""Sorting nexins"""	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.1045G>A	6.37:g.158342658G>A	ENSP00000376024:p.Val349Ile		Somatic					p.V349I	NM_016224	NP_057308	WXS	Illumina GAIIx	Phase_I	Q9Y5X1	SNX9_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)	9	1218	+		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)	349			PX.		Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Missense_Mutation	SNP	ENST00000392185.3	37	c.1045G>A	CCDS5253.1	.	.	.	.	.	.	.	.	.	.	G	8.882	0.951906	0.18431	.	.	ENSG00000130340	ENST00000539592;ENST00000392185;ENST00000252631	T	0.42131	0.98	5.68	0.548	0.17208	Phox homologous domain (5);	0.183339	0.47455	D	0.000233	T	0.21145	0.0509	L	0.38175	1.15	0.58432	D	0.999999	B	0.23937	0.094	B	0.25140	0.058	T	0.23297	-1.0192	10	0.18710	T	0.47	-26.299	20.9179	0.99941	0.0:0.6978:0.3022:0.0	.	349	Q9Y5X1	SNX9_HUMAN	I	349;349;149	ENSP00000376024:V349I	ENSP00000252631:V149I	V	+	1	0	SNX9	158262646	1.000000	0.71417	0.574000	0.28523	0.732000	0.41865	3.692000	0.54727	2.159000	0.67721	0.459000	0.35465	GTT		0.428	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1			24	44	0	0	0	1	0	24	44				
MIER2	54531	broad.mit.edu	37	19	334487	334487	+	Silent	SNP	C	C	T			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr19:334487C>T	ENST00000264819.4	-	3	166	c.156G>A	c.(154-156)caG>caA	p.Q52Q	MIER2_ENST00000592722.1_5'UTR	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	52					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACTGTAGTTCTGTGACAGGA	0.597																																						uc002lok.1																			0				endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22						c.(154-156)caG>caA		Homo sapiens mesoderm induction early response 1, family member 2 (MIER2), mRNA.							131.0	112.0	118.0					19																	334487		2203	4300	6503	SO:0001819	synonymous_variant	54531				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding	g.chr19:334487C>T	AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"""KIAA1193"""	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.156G>A	19.37:g.334487C>T			Somatic					p.Q52Q	NM_017550	NP_060020	WXS	Illumina GAIIx	Phase_I	Q8N344	MIER2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	2	165	-		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)	52					Q9ULM7	Silent	SNP	ENST00000264819.4	37	c.156G>A	CCDS32855.1																																																																																				0.597	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		21	86	0	0	0	1	0	21	86				
TRAK1	22906	broad.mit.edu	37	3	42167045	42167045	+	Missense_Mutation	SNP	T	T	G			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr3:42167045T>G	ENST00000327628.5	+	2	625	c.225T>G	c.(223-225)atT>atG	p.I75M	TRAK1_ENST00000487159.1_3'UTR	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	75	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CACCTCTCATTTCTCCAGATG	0.463																																					GBM(44;195 884 22595 31865 41850)	uc003cky.3																			0				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						c.(223-225)atT>atG		Homo sapiens trafficking protein, kinesin binding 1 (TRAK1), transcript variant 1, mRNA.							148.0	139.0	142.0					3																	42167045		1962	4151	6113	SO:0001583	missense	22906				endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus		g.chr3:42167045T>G		CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.225T>G	3.37:g.42167045T>G	ENSP00000328998:p.Ile75Met		Somatic				TRAK1_uc011azh.2_Missense_Mutation_p.I75M|TRAK1_uc011azi.2_Missense_Mutation_p.I75M	p.I75M	NM_001042646	NP_001036111	WXS	Illumina GAIIx	Phase_I	Q9UPV9	TRAK1_HUMAN			1	441	+			75			HAP1 N-terminal.		E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	c.225T>G	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.449698	0.43531	.	.	ENSG00000182606	ENST00000327628;ENST00000543338	T	0.16897	2.31	5.73	-0.277	0.12898	.	0.272610	0.33670	N	0.004662	T	0.09686	0.0238	N	0.22421	0.69	0.80722	D	1	P;B	0.39022	0.655;0.304	B;B	0.39771	0.309;0.214	T	0.25433	-1.0132	10	0.30078	T	0.28	.	6.4178	0.21725	0.0:0.3471:0.1282:0.5246	.	75;75	B7Z347;Q9UPV9	.;TRAK1_HUMAN	M	75	ENSP00000328998:I75M	ENSP00000328998:I75M	I	+	3	3	TRAK1	42142049	0.981000	0.34729	0.994000	0.49952	0.997000	0.91878	0.160000	0.16462	-0.037000	0.13646	0.533000	0.62120	ATT		0.463	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		50	99	0	0	0	1	0	50	99				
MYH13	8735	broad.mit.edu	37	17	10265497	10265497	+	Missense_Mutation	SNP	C	C	T	rs202246911		TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr17:10265497C>T	ENST00000418404.3	-	4	606	c.443G>A	c.(442-444)cGc>cAc	p.R148H	MYH13_ENST00000252172.4_Missense_Mutation_p.R148H			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	148	Myosin motor.				cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						GGCCTCCTGGCGCTTTTTGCC	0.527																																						uc002gmk.1																			0				breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						c.(442-444)cGc>cAc		Homo sapiens myosin, heavy chain 13, skeletal muscle (MYH13), mRNA.		C	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	82.0	92.0	88.0		443	4.1	1.0	17		88	1,8593	1.2+/-3.3	0,1,4296	no	missense	MYH13	NM_003802.2	29	0,4,6496	TT,TC,CC		0.0116,0.0681,0.0308	probably-damaging	148/1939	10265497	4,12996	2203	4297	6500	SO:0001583	missense	8735				muscle contraction	muscle myosin complex|myofibril|myosin filament	ATP binding|actin binding|calmodulin binding|microfilament motor activity	g.chr17:10265497C>T	AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788		"""Myosins / Myosin superfamily : Class II"""	7571	protein-coding gene	gene with protein product	"""extraocular muscle myosin heavy chain"", ""extraocular myosin heavy chain"""	603487	"""myosin, heavy polypeptide 13, skeletal muscle"""			9806854	Standard	NM_003802		Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.443G>A	17.37:g.10265497C>T	ENSP00000404570:p.Arg148His		Somatic					p.R148H	NM_003802	NP_003793	WXS	Illumina GAIIx	Phase_I	Q9UKX3	MYH13_HUMAN			4	533	-			148			Myosin head-like.		O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	c.443G>A	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.302836	0.81136	6.81E-4	1.16E-4	ENSG00000006788	ENST00000252172	D	0.88354	-2.37	4.08	4.08	0.47627	Myosin head, motor domain (2);	.	.	.	.	D	0.96228	0.8770	H	0.96430	3.82	0.46061	D	0.998848	D	0.89917	1.0	D	0.77004	0.989	D	0.97787	1.0236	9	0.87932	D	0	.	16.8101	0.85717	0.0:1.0:0.0:0.0	.	148	Q9UKX3	MYH13_HUMAN	H	148	ENSP00000252172:R148H	ENSP00000252172:R148H	R	-	2	0	MYH13	10206222	1.000000	0.71417	1.000000	0.80357	0.647000	0.38526	7.492000	0.81482	2.272000	0.75746	0.313000	0.20887	CGC		0.527	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442255.1	NM_003802		63	121	0	0	0	1	0	63	121				
PLEKHA5	54477	broad.mit.edu	37	12	19408022	19408022	+	Missense_Mutation	SNP	A	A	G			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr12:19408022A>G	ENST00000299275.6	+	5	361	c.355A>G	c.(355-357)Ata>Gta	p.I119V	PLEKHA5_ENST00000539256.1_5'UTR|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.I11V|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.I119V|PLEKHA5_ENST00000309364.4_Missense_Mutation_p.I119V|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.I119V|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.I119V|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.I119V|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.I11V|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.I119V	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	119					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GGAACGGCCAATAAGTATGAT	0.358																																					Pancreas(196;329 2193 11246 14234 19524)	uc010sie.2																			0				autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						c.(355-357)Ata>Gta		Homo sapiens pleckstrin homology domain containing, family A member 5 (PLEKHA5), transcript variant 2, mRNA.							120.0	112.0	115.0					12																	19408022		2203	4300	6503	SO:0001583	missense	54477						1-phosphatidylinositol binding|protein binding	g.chr12:19408022A>G	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.355A>G	12.37:g.19408022A>G	ENSP00000299275:p.Ile119Val		Somatic				PLEKHA5_uc001rea.3_Missense_Mutation_p.I119V|PLEKHA5_uc001reb.3_Missense_Mutation_p.I119V|PLEKHA5_uc009zin.3_5'UTR|PLEKHA5_uc010sig.2_Missense_Mutation_p.I11V|PLEKHA5_uc010sih.1_Missense_Mutation_p.I11V|PLEKHA5_uc021qvy.1_Missense_Mutation_p.I11V	p.I119V	NM_001143821	NP_001137293	WXS	Illumina GAIIx	Phase_I	Q9HAU0	PKHA5_HUMAN			4	463	+	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)		119					A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	c.355A>G	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	2.445	-0.327616	0.05314	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000412219;ENST00000429027;ENST00000299275;ENST00000538714;ENST00000538305;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.28666	2.75;2.75;2.75;2.75;2.75;2.75;2.75;1.6;3.04;3.04;3.03	4.87	2.47	0.30058	.	0.455403	0.24625	N	0.036935	T	0.10465	0.0256	N	0.08118	0	0.48901	D	0.999728	B;B;B;B;B;B	0.11235	0.004;0.001;0.001;0.002;0.001;0.002	B;B;B;B;B;B	0.11329	0.006;0.003;0.002;0.002;0.003;0.004	T	0.25152	-1.0140	10	0.02654	T	1	-7.9378	3.3669	0.07207	0.5517:0.2052:0.2431:0.0	.	119;11;11;119;119;119	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;Q9HAU0;Q9HAU0-2	.;.;.;.;PKHA5_HUMAN;.	V	119;119;119;119;119;119;119;119;119;11;11;11;11	ENSP00000325155:I119V;ENSP00000347560:I119V;ENSP00000352104:I119V;ENSP00000311239:I119V;ENSP00000404296:I119V;ENSP00000299275:I119V;ENSP00000439673:I119V;ENSP00000446308:I11V;ENSP00000400411:I11V;ENSP00000439837:I11V;ENSP00000440371:I11V	ENSP00000299275:I119V	I	+	1	0	PLEKHA5	19299289	0.098000	0.21812	0.744000	0.31058	0.977000	0.68977	0.552000	0.23376	0.336000	0.23639	0.377000	0.23210	ATA		0.358	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		21	57	0	0	0	1	0	21	57				
PPL	5493	broad.mit.edu	37	16	4934540	4934540	+	Silent	SNP	G	G	A			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr16:4934540G>A	ENST00000345988.2	-	22	4205	c.4116C>T	c.(4114-4116)gcC>gcT	p.A1372A	PPL_ENST00000590782.2_Silent_p.A1370A	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1372					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CGATGCTCTCGGCAAAGGCGC	0.677																																						uc002cyd.1																			0				breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						c.(4114-4116)gcC>gcT		Homo sapiens periplakin (PPL), mRNA.							92.0	99.0	97.0					16																	4934540		2197	4300	6497	SO:0001819	synonymous_variant	5493				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton	g.chr16:4934540G>A	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.4116C>T	16.37:g.4934540G>A			Somatic					p.A1372A	NM_002705	NP_002696	WXS	Illumina GAIIx	Phase_I	O60437	PEPL_HUMAN			21	4206	-			1372					O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	c.4116C>T	CCDS10526.1																																																																																				0.677	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		29	211	0	0	0	1	0	29	211				
CYP4F24P	388514	broad.mit.edu	37	19	15871692	15871692	+	lincRNA	SNP	G	G	A			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr19:15871692G>A	ENST00000595525.1	+	0	508																											GAGTTGAAGCGGAAGGGGTTG	0.577																																						uc002nbo.3																			0													Homo sapiens cytochrome P450, family 4, subfamily F, polypeptide 24, pseudogene (CYP4F24P), non-coding RNA.																																						388514							g.chr19:15871692G>A																													19.37:g.15871692G>A			Somatic								WXS	Illumina GAIIx	Phase_I					8		-									RNA	SNP	ENST00000595525.1	37	c.1316C>T																																																																																					0.577	LLNLR-249E10.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000472008.1			25	54	0	0	0	1	0	25	54				
LEMD1	93273	broad.mit.edu	37	1	205350961	205350961	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr1:205350961G>A	ENST00000367153.4	-	6	473	c.371C>T	c.(370-372)aCc>aTc	p.T124I	LEMD1_ENST00000367152.1_Missense_Mutation_p.T83I|LEMD1_ENST00000367149.3_Missense_Mutation_p.P36S|LEMD1_ENST00000367151.2_Missense_Mutation_p.T83I|LEMD1-AS1_ENST00000447832.1_RNA|LEMD1_ENST00000476884.1_5'UTR|LEMD1_ENST00000391936.2_Missense_Mutation_p.P77S|LEMD1_ENST00000367154.1_Missense_Mutation_p.P77S	NM_001199050.1	NP_001185979.1	Q68G75	LEMD1_HUMAN	LEM domain containing 1	124						integral component of membrane (GO:0016021)				breast(1)|lung(2)	3	Breast(84;0.247)		BRCA - Breast invasive adenocarcinoma(75;0.0938)			TGTGATTCTGGTGCTTGGTGC	0.512																																						uc001hcj.2																			0				breast(1)|lung(2)	3						c.(370-372)aCc>aTc		Homo sapiens LEM domain containing 1 (LEMD1), transcript variant 1, mRNA.							221.0	193.0	203.0					1																	205350961		2203	4300	6503	SO:0001583	missense	93273					integral to membrane|nuclear envelope		g.chr1:205350961G>A		CCDS30986.1, CCDS55677.1, CCDS55678.1, CCDS55679.1	1q32.1	2009-03-25			ENSG00000186007	ENSG00000186007			18725	protein-coding gene	gene with protein product	"""cancer/testis antigen 50"""	610480				15254688	Standard	NM_001199050		Approved	LEMP-1, CT50	uc001hcj.2	Q68G75	OTTHUMG00000037201	ENST00000367153.4:c.371C>T	1.37:g.205350961G>A	ENSP00000356121:p.Thr124Ile		Somatic				LEMD1_uc001hcl.2_Missense_Mutation_p.T83I|LEMD1_uc001hci.2_Missense_Mutation_p.P77S|LEMD1_uc001hcm.2_Non-coding_Transcript|LEMD1_uc001hcn.2_Missense_Mutation_p.P36S|LEMD1_uc001hck.2_Non-coding_Transcript|LOC284576_uc001hch.1_Intron	p.T124I	NM_001199050	NP_001185979	WXS	Illumina GAIIx	Phase_I	Q68G75	LEMD1_HUMAN	BRCA - Breast invasive adenocarcinoma(75;0.0938)		5	506	-	Breast(84;0.247)		124					Q6L9T9|Q6L9U0|Q6L9U1|Q6L9U2|Q6L9U3|Q6L9U4	Missense_Mutation	SNP	ENST00000367153.4	37	c.371C>T	CCDS55679.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.76|11.76	1.735113|1.735113	0.30774|0.30774	.|.	.|.	ENSG00000186007|ENSG00000186007	ENST00000367154;ENST00000391936;ENST00000367149|ENST00000367152;ENST00000367153;ENST00000367151	T;T;T|T;T;T	0.58358|0.45668	0.95;0.95;0.34|0.89;0.89;0.89	4.31|4.31	-1.56|-1.56	0.08532|0.08532	.|.	.|1.535450	.|0.03609	.|N	.|0.234517	T|T	0.28928|0.28928	0.0718|0.0718	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|B;B	0.26483|0.16396	0.15|0.017;0.002	B|B;B	0.23852|0.10450	0.049|0.005;0.002	T|T	0.20338|0.20338	-1.0278|-1.0278	8|9	0.87932|0.46703	D|T	0|0.11	-22.5303|-22.5303	4.7233|4.7233	0.12929|0.12929	0.4016:0.1537:0.4447:0.0|0.4016:0.1537:0.4447:0.0	.|.	77|83;124	Q68G75-5|Q68G75-3;Q68G75	.|.;LEMD1_HUMAN	S|I	77;77;36|83;124;83	ENSP00000356122:P77S;ENSP00000375801:P77S;ENSP00000356117:P36S|ENSP00000356120:T83I;ENSP00000356121:T124I;ENSP00000356119:T83I	ENSP00000356117:P36S|ENSP00000356119:T83I	P|T	-|-	1|2	0|0	LEMD1|LEMD1	203617584|203617584	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-0.071000|-0.071000	0.11505|0.11505	-0.383000|-0.383000	0.07858|0.07858	-0.163000|-0.163000	0.13421|0.13421	CCA|ACC		0.512	LEMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090401.1	NM_001001552		54	108	0	0	0	1	0	54	108				
LPAL2	80350	broad.mit.edu	37	6	160887731	160887732	+	RNA	INS	-	-	C			TCGA-ET-A40S-01A-11D-A23M-08	TCGA-ET-A40S-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ca41acc-aede-46b8-9b84-0e7db08d92f3	81b90d1a-50de-4b44-9223-da38169863a6	g.chr6:160887731_160887732insC	ENST00000335388.5	-	0	2041					NR_028092.1		Q16609	LPAL2_HUMAN	lipoprotein, Lp(a)-like 2, pseudogene							extracellular region (GO:0005576)				large_intestine(1)|lung(4)	5		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)		cctaatgctatcctcccccctc	0.495																																						uc003qtj.2																			0				large_intestine(1)|lung(4)	5								Homo sapiens lipoprotein, Lp(a)-like 2, pseudogene (LPAL2), transcript variant 2, non-coding RNA.																																						80350							g.chr6:160887731_160887732insC	U19517		6q26-q27	2010-10-27	2010-10-27	2004-02-18	ENSG00000213071	ENSG00000213071			21210	pseudogene	pseudogene		611682	"""apolipoprotein A-like"", ""lipoprotein, Lp(a)-like 2"""	APOAL		7749817, 7679504	Standard	NR_028092		Approved	APOARGC	uc011efy.2	Q16609	OTTHUMG00000015952		6.37:g.160887733_160887733dupC			Somatic								WXS	Illumina GAIIx	Phase_I				OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	9		-		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.214)						E1P5B4	RNA	INS	ENST00000335388.5	37	c.1823_1824insG																																																																																					0.495	LPAL2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000042950.1	NM_024492		2	4						2	4	---	---	---	---
