#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
APOA2	336	genome.wustl.edu	37	1	161192845	161192846	+	Intron	INS	-	-	CA	rs72374375|rs17244502|rs60433002|rs57498167|rs141599125		TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr1:161192845_161192846insCA	ENST00000367990.3	-	3	110				APOA2_ENST00000463812.1_Intron|TOMM40L_ENST00000367988.3_5'Flank|APOA2_ENST00000491350.1_Intron|APOA2_ENST00000470459.2_Intron|APOA2_ENST00000464492.1_Intron|APOA2_ENST00000468465.1_Intron	NM_001643.1	NP_001634.1	P02652	APOA2_HUMAN	apolipoprotein A-II						acute inflammatory response (GO:0002526)|cellular lipid metabolic process (GO:0044255)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|high-density lipoprotein particle assembly (GO:0034380)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol import (GO:0060621)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cholesterol transporter activity (GO:0060695)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of lipase activity (GO:0060192)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of very-low-density lipoprotein particle remodeling (GO:0010903)|organ regeneration (GO:0031100)|peptidyl-methionine modification (GO:0018206)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid catabolic process (GO:0009395)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of lipid catabolic process (GO:0050996)|protein folding (GO:0006457)|protein oxidation (GO:0018158)|regulation of intestinal cholesterol absorption (GO:0030300)|regulation of protein stability (GO:0031647)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|viral process (GO:0016032)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein receptor binding (GO:0034190)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor binding (GO:0070653)|lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|phospholipid binding (GO:0005543)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(2)|skin(2)	6	all_cancers(52;1.86e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			AAGCTCCTGCCcacacacacac	0.55																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0				CCDS1226.1	1q23.3	2013-01-24			ENSG00000158874	ENSG00000158874		"""Apolipoproteins"""	601	protein-coding gene	gene with protein product		107670				2415515	Standard	NM_001643		Approved		uc001fzc.1	P02652	OTTHUMG00000034346	ENST00000367990.3:c.53-5->TG	1.37:g.161192854_161192855dupCA		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R524	RNA	INS	-	NULL	ENST00000367990.3	37	NULL	CCDS1226.1	1																																																																																			APOA2	-	-	ENSG00000158874		0.550	APOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APOA2	HGNC	protein_coding	OTTHUMT00000083037.1	18	0.00	0	-	NM_001643		161192845	161192846	-1	no_errors	ENST00000481413	ensembl	human	known	69_37n	rna	34	19.05	8	INS	0.006:0.011	CA
ATG5	9474	genome.wustl.edu	37	6	106633695	106633695	+	3'UTR	SNP	C	C	A			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr6:106633695C>A	ENST00000369076.3	-	0	1871				ATG5_ENST00000360666.4_3'UTR|ATG5_ENST00000343245.3_3'UTR|ATG5_ENST00000369070.1_3'UTR|ATG5_ENST00000475645.1_5'UTR	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5						apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		ATATCCACCCCATGCCAATGA	0.368																																						dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"""APG5 (autophagy 5, S. cerevisiae)-like"", ""APG5 autophagy 5-like (S. cerevisiae)"", ""ATG5 autophagy related 5 homolog (S. cerevisiae)"""	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.*720G>T	6.37:g.106633695C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	RNA	SNP	-	NULL	ENST00000369076.3	37	NULL	CCDS5055.1	6																																																																																			ATG5	-	-	ENSG00000057663		0.368	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATG5	HGNC	protein_coding	OTTHUMT00000043476.1	8	0.00	0	C	NM_004849		106633695	106633695	-1	no_errors	ENST00000475645	ensembl	human	known	69_37n	rna	13	23.53	4	SNP	0.000	A
BATF3	55509	genome.wustl.edu	37	1	212870819	212870819	+	Intron	SNP	T	T	G			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr1:212870819T>G	ENST00000243440.1	-	2	313				BATF3_ENST00000478275.1_5'UTR	NM_018664.2	NP_061134.1	Q9NR55	BATF3_HUMAN	basic leucine zipper transcription factor, ATF-like 3						dendritic cell differentiation (GO:0097028)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to virus (GO:0009615)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0046)|all cancers(67;0.00785)|GBM - Glioblastoma multiforme(131;0.0731)|Epithelial(68;0.0781)		TGGGTGGGGGTGGGGGGCGGT	0.507																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AF255346	CCDS1508.1	1q32.3	2013-01-10			ENSG00000123685	ENSG00000123685		"""basic leucine zipper proteins"""	28915	protein-coding gene	gene with protein product	"""Jun dimerization protein 1"""	612470				10878360, 12087103	Standard	NM_018664		Approved	JUNDM1, SNFT, JDP1	uc001hjl.2	Q9NR55	OTTHUMG00000036807	ENST00000243440.1:c.91-412A>C	1.37:g.212870819T>G		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000243440.1	37	NULL	CCDS1508.1	1																																																																																			BATF3	-	-	ENSG00000123685		0.507	BATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BATF3	HGNC	protein_coding	OTTHUMT00000089403.1	19	0.00	0	T	NM_018664		212870819	212870819	-1	no_errors	ENST00000478275	ensembl	human	known	69_37n	rna	4	66.67	8	SNP	0.000	G
CDC27	996	genome.wustl.edu	37	17	45234350	45234350	+	Silent	SNP	C	C	T			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr17:45234350C>T	ENST00000066544.3	-	7	864	c.771G>A	c.(769-771)caG>caA	p.Q257Q	CDC27_ENST00000446365.2_Silent_p.Q196Q|CDC27_ENST00000531206.1_Silent_p.Q257Q|CDC27_ENST00000527547.1_Silent_p.Q257Q|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	257					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.Q257Q(3)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TATTTTGAACCTGTTTAGATA	0.383																																						dbGAP											3	Substitution - coding silent(3)	prostate(3)											57.0	63.0	61.0					17																	45234350		2198	4294	6492	-	-	-	SO:0001819	synonymous_variant	0			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.771G>A	17.37:g.45234350C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	G3V1C4|Q16349|Q96F35	Splice_Site	SNP	-	e7-1	ENST00000066544.3	37	c.631-1	CCDS11509.1	17																																																																																			CDC27	-	-	ENSG00000004897		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	CDC27	HGNC	protein_coding	OTTHUMT00000389742.2	39	0.00	0	C			45234350	45234350	-1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000575483	ensembl	human	novel	69_37n	splice_site	44	10.20	5	SNP	1.000	T
CDK5RAP3	80279	genome.wustl.edu	37	17	46053334	46053334	+	Silent	SNP	A	A	G	rs202125432	byFrequency	TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr17:46053334A>G	ENST00000338399.4	+	8	859	c.753A>G	c.(751-753)gaA>gaG	p.E251E	CDK5RAP3_ENST00000536708.2_Silent_p.E276E|RP11-6N17.9_ENST00000582262.1_RNA	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	251					brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)	p.E251E(1)		NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						CTGTGGTGGAACGACCCCACC	0.602																																						dbGAP											1	Substitution - coding silent(1)	prostate(1)																																								-	-	-	SO:0001819	synonymous_variant	0			AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465			18673	protein-coding gene	gene with protein product	"""ischemic heart CDK5 activator-binding protein C53"", ""LXXLL/leucine-zipper-containing ARFbinding protein"""	608202				10721722	Standard	NM_176096		Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.753A>G	17.37:g.46053334A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	Silent	SNP	pfam_DUF773	p.E251	ENST00000338399.4	37	c.753	CCDS42356.1	17																																																																																			CDK5RAP3	-	pfam_DUF773	ENSG00000108465		0.602	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDK5RAP3	HGNC	protein_coding	OTTHUMT00000442913.1	47	0.00	0	A	NM_176096		46053334	46053334	+1	no_errors	ENST00000338399	ensembl	human	known	69_37n	silent	87	10.31	10	SNP	1.000	G
CENPP	401541	genome.wustl.edu	37	9	95094596	95094596	+	Silent	SNP	G	G	A			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr9:95094596G>A	ENST00000375587.3	+	2	767	c.252G>A	c.(250-252)caG>caA	p.Q84Q		NM_001012267.1	NP_001012267.1	Q6IPU0	CENPP_HUMAN	centromere protein P	84					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(1)	16						ACTCCAAGCAGACAGAAGACC	0.333																																						dbGAP											0													56.0	57.0	57.0					9																	95094596		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK091247	CCDS35063.1, CCDS69618.1	9q22.31	2013-11-05			ENSG00000188312	ENSG00000188312			32933	protein-coding gene	gene with protein product		611505				16622419, 16622420	Standard	NM_001286969		Approved	RP11-19J3.3, CENP-P	uc004arz.3	Q6IPU0	OTTHUMG00000020228	ENST00000375587.3:c.252G>A	9.37:g.95094596G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KRA5|B3KS17|Q5T9F8|Q5T9F9	Silent	SNP	NULL	p.Q84	ENST00000375587.3	37	c.252	CCDS35063.1	9																																																																																			CENPP	-	NULL	ENSG00000188312		0.333	CENPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	CENPP	HGNC	protein_coding	OTTHUMT00000053098.1	39	0.00	0	G	NM_001012267		95094596	95094596	+1	no_errors	ENST00000375587	ensembl	human	known	69_37n	silent	46	20.69	12	SNP	0.280	A
CLCA4	22802	genome.wustl.edu	37	1	87045231	87045231	+	Missense_Mutation	SNP	A	A	G			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr1:87045231A>G	ENST00000370563.3	+	13	2359	c.2317A>G	c.(2317-2319)Aca>Gca	p.T773A	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	773					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		GATTATTCTTACATGGACAGC	0.413																																						dbGAP											0													135.0	120.0	125.0					1																	87045231		1908	4127	6035	-	-	-	SO:0001583	missense	0			AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2317A>G	1.37:g.87045231A>G	ENSP00000359594:p.Thr773Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	pfam_Cl_channel_Ca,pfam_DUF1973,pfam_VWF_A,superfamily_Fibronectin_type3,smart_VWF_A,pfscan_VWF_A,tigrfam_CaCC_prot	p.T773A	ENST00000370563.3	37	c.2317	CCDS41355.1	1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678650	0.47886	.	.	ENSG00000016602	ENST00000370563	T	0.03212	4.01	5.5	2.98	0.34508	.	0.141960	0.46442	D	0.000295	T	0.09905	0.0243	M	0.87682	2.9	0.80722	D	1	D;D	0.67145	0.98;0.996	P;D	0.64595	0.881;0.927	T	0.01068	-1.1462	10	0.66056	D	0.02	-19.6794	9.9434	0.41593	0.627:0.0:0.0:0.373	.	325;773	Q9NXP1;Q14CN2	.;CLCA4_HUMAN	A	773	ENSP00000359594:T773A	ENSP00000359594:T773A	T	+	1	0	CLCA4	86817819	0.017000	0.18338	0.951000	0.38953	0.544000	0.35116	1.571000	0.36450	0.868000	0.35678	0.460000	0.39030	ACA	CLCA4	-	superfamily_Fibronectin_type3,tigrfam_CaCC_prot	ENSG00000016602		0.413	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CLCA4	HGNC	protein_coding	OTTHUMT00000028292.1	39	0.00	0	A	NM_012128		87045231	87045231	+1	no_errors	ENST00000370563	ensembl	human	known	69_37n	missense	47	20.34	12	SNP	0.922	G
COL6A5	256076	genome.wustl.edu	37	3	130159257	130159257	+	Silent	SNP	A	A	G			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr3:130159257A>G	ENST00000432398.2	+	35	6569	c.6075A>G	c.(6073-6075)acA>acG	p.T2025T	COL6A5_ENST00000265379.6_Silent_p.T2025T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2025	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						AGATGGGTACAGTAAAAACAG	0.398																																						dbGAP											0													90.0	85.0	86.0					3																	130159257		1882	4101	5983	-	-	-	SO:0001819	synonymous_variant	0			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.6075A>G	3.37:g.130159257A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	pfam_VWF_A,smart_VWF_A,pfscan_VWF_A	p.S277G	ENST00000432398.2	37	c.829		3	.	.	.	.	.	.	.	.	.	.	A	0.179	-1.064280	0.01934	.	.	ENSG00000172752	ENST00000512836	.	.	.	5.76	-8.09	0.01090	.	.	.	.	.	T	0.25531	0.0621	.	.	.	0.19300	N	0.999971	.	.	.	.	.	.	T	0.34030	-0.9845	4	.	.	.	.	8.2862	0.31930	0.5339:0.247:0.2191:0.0	.	.	.	.	G	277	.	.	S	+	1	0	COL6A5	131641947	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-2.163000	0.01276	-1.049000	0.03234	0.533000	0.62120	AGT	COL6A5	-	pfam_VWF_A,smart_VWF_A,pfscan_VWF_A	ENSG00000172752		0.398	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	COL6A5	HGNC	protein_coding		50	0.00	0	A	NM_153264		130159257	130159257	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000512836	ensembl	human	putative	69_37n	missense	54	19.40	13	SNP	0.000	G
FAM65C	140876	genome.wustl.edu	37	20	49209055	49209055	+	Silent	SNP	C	C	G			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr20:49209055C>G	ENST00000327979.2	-	19	2802	c.2391G>C	c.(2389-2391)gcG>gcC	p.A797A	FAM65C_ENST00000462842.1_5'Flank|FAM65C_ENST00000535356.1_Silent_p.A801A|FAM65C_ENST00000045083.2_Silent_p.A797A			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	797										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGGCCTGTCCCGCACAGTGAA	0.622																																						dbGAP											0													18.0	20.0	19.0					20																	49209055		1933	4128	6061	-	-	-	SO:0001819	synonymous_variant	0			AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062			16168	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 175"", ""chromosome 20 open reading frame 176"""	C20orf175, C20orf176			Standard	XM_005260294		Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.2391G>C	20.37:g.49209055C>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5QPB6|Q9NQQ2	Silent	SNP	superfamily_ARM-type_fold,superfamily_Chemokine_IL8-like_dom	p.A801	ENST00000327979.2	37	c.2403	CCDS13431.2	20																																																																																			FAM65C	-	NULL	ENSG00000042062		0.622	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM65C	HGNC	protein_coding	OTTHUMT00000257962.1	60	0.00	0	C			49209055	49209055	-1	no_errors	ENST00000535356	ensembl	human	known	69_37n	silent	44	38.89	28	SNP	0.000	G
FLAD1	80308	genome.wustl.edu	37	1	154960671	154960671	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr1:154960671G>A	ENST00000292180.3	+	2	785	c.463G>A	c.(463-465)Gag>Aag	p.E155K	FLAD1_ENST00000368433.1_Missense_Mutation_p.E155K|FLAD1_ENST00000487371.1_3'UTR|FLAD1_ENST00000315144.10_Missense_Mutation_p.E58K|FLAD1_ENST00000368431.3_Missense_Mutation_p.E56K|FLAD1_ENST00000368432.1_Missense_Mutation_p.E58K|FLAD1_ENST00000295530.2_5'UTR|FLAD1_ENST00000405236.2_Missense_Mutation_p.E56K|FLAD1_ENST00000368428.1_5'Flank	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	155	Molybdenum cofactor biosynthesis protein- like.				FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)			endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			TGTACCTGATGAGGTAGCCAC	0.572																																						dbGAP											0													124.0	110.0	115.0					1																	154960671		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"""Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)"", ""FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)"", ""flavin adenine dinucleotide synthetase"""				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.463G>A	1.37:g.154960671G>A	ENSP00000292180:p.Glu155Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	pfam_Mopterin-bd,pfam_PAPS_reduct,superfamily_Mopterin-bd,smart_Mopterin-bd,pirsf_FAD_synth_Mopterin-bd	p.E155K	ENST00000292180.3	37	c.463	CCDS1078.1	1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.275431	0.80580	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000368431;ENST00000292180;ENST00000405236	T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.84	5.84	0.93424	Molybdopterin binding (4);	0.236935	0.42964	D	0.000639	T	0.79787	0.4506	L	0.53617	1.68	0.36785	D	0.884569	P;P	0.51653	0.947;0.928	P;P	0.53988	0.739;0.553	T	0.80533	-0.1340	10	0.54805	T	0.06	-21.145	19.7483	0.96259	0.0:0.0:1.0:0.0	.	155;56	Q8NFF5;Q8NFF5-4	FAD1_HUMAN;.	K	155;58;58;56;155;56	ENSP00000357418:E155K;ENSP00000317296:E58K;ENSP00000357417:E58K;ENSP00000357416:E56K;ENSP00000292180:E155K;ENSP00000384323:E56K	ENSP00000292180:E155K	E	+	1	0	FLAD1	153227295	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	4.889000	0.63171	2.779000	0.95612	0.655000	0.94253	GAG	FLAD1	-	pfam_Mopterin-bd,superfamily_Mopterin-bd,smart_Mopterin-bd,pirsf_FAD_synth_Mopterin-bd	ENSG00000160688		0.572	FLAD1-001	NOVEL	basic|CCDS	protein_coding	FLAD1	HGNC	protein_coding	OTTHUMT00000091089.1	145	0.00	0	G	NM_025207		154960671	154960671	+1	no_errors	ENST00000292180	ensembl	human	known	69_37n	missense	119	25.62	41	SNP	1.000	A
KIAA0319	9856	genome.wustl.edu	37	6	24596724	24596724	+	Missense_Mutation	SNP	C	C	T			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr6:24596724C>T	ENST00000378214.3	-	3	702	c.178G>A	c.(178-180)Gct>Act	p.A60T	KIAA0319_ENST00000430948.2_Missense_Mutation_p.A15T|KIAA0319_ENST00000535378.1_Missense_Mutation_p.A51T|KIAA0319_ENST00000537886.1_Missense_Mutation_p.A60T|KIAA0319_ENST00000543707.1_Missense_Mutation_p.A60T	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	60	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						TCACAGCAAGCGGCCGTGCAG	0.567																																						dbGAP											0													70.0	60.0	63.0					6																	24596724		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.178G>A	6.37:g.24596724C>T	ENSP00000367459:p.Ala60Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	pfam_PKD/REJ-like,superfamily_PKD_dom,smart_MANSC_N,smart_Fibronectin_type3,smart_PKD/Chitinase_dom,pfscan_MANSC,pfscan_PKD_dom	p.A60T	ENST00000378214.3	37	c.178	CCDS34348.1	6	.	.	.	.	.	.	.	.	.	.	C	21.1	4.103592	0.76983	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.10573	2.86;2.89;2.86;2.87;2.87	3.7	3.7	0.42460	Seven cysteines (1);Seven cysteines, N-terminal (1);	0.000000	0.64402	D	0.000018	T	0.23330	0.0564	M	0.72894	2.215	0.48830	D	0.999713	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.996	T	0.04737	-1.0930	10	0.72032	D	0.01	-15.1814	15.6293	0.76888	0.0:1.0:0.0:0.0	.	60;51;60	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	T	60;51;15;60;60	ENSP00000439700:A60T;ENSP00000442403:A51T;ENSP00000401086:A15T;ENSP00000367459:A60T;ENSP00000437656:A60T	ENSP00000367459:A60T	A	-	1	0	KIAA0319	24704703	0.999000	0.42202	0.648000	0.29521	0.551000	0.35334	4.426000	0.59882	1.874000	0.54306	0.514000	0.50259	GCT	KIAA0319	-	smart_MANSC_N,pfscan_MANSC	ENSG00000137261		0.567	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA0319	HGNC	protein_coding	OTTHUMT00000040009.1	24	0.00	0	C	NM_014809		24596724	24596724	-1	no_errors	ENST00000378214	ensembl	human	known	69_37n	missense	35	27.08	13	SNP	0.996	T
LACE1	246269	genome.wustl.edu	37	6	108843570	108843570	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr6:108843570G>A	ENST00000368977.4	+	13	1574	c.1388G>A	c.(1387-1389)cGa>cAa	p.R463Q		NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1	463						mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)		ACAATTTCCCGACTCACGGAA	0.383																																						dbGAP											0													71.0	64.0	67.0					6																	108843570		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF520418	CCDS5067.1	6q22.1	2006-11-10			ENSG00000135537	ENSG00000135537			16411	protein-coding gene	gene with protein product	"""ATPase family gene 1 homolog (S. cerevisiae)"""					12079282	Standard	XM_005266885		Approved	AFG1	uc003psj.3	Q8WV93	OTTHUMG00000015324	ENST00000368977.4:c.1388G>A	6.37:g.108843570G>A	ENSP00000357973:p.Arg463Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N6A3	Missense_Mutation	SNP	pfam_ATPase_AFG1-like	p.R463Q	ENST00000368977.4	37	c.1388	CCDS5067.1	6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.289954|5.289954	0.95546|0.95546	.|.	.|.	ENSG00000135537|ENSG00000135537	ENST00000421954|ENST00000368977	.|.	.|.	.|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.89846|0.89846	0.6833|0.6833	H|H	0.97465|0.97465	4.01|4.01	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.92579|0.92579	0.6073|0.6073	5|9	.|0.87932	.|D	.|0	-8.8417|-8.8417	19.7753|19.7753	0.96389|0.96389	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|463	.|Q8WV93	.|LACE1_HUMAN	N|Q	331|463	.|.	.|ENSP00000357973:R463Q	D|R	+|+	1|2	0|0	LACE1|LACE1	108950263|108950263	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.623000|0.623000	0.37688|0.37688	9.298000|9.298000	0.96132|0.96132	2.777000|2.777000	0.95525|0.95525	0.655000|0.655000	0.94253|0.94253	GAC|CGA	LACE1	-	NULL	ENSG00000135537		0.383	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LACE1	HGNC	protein_coding	OTTHUMT00000041719.4	35	0.00	0	G	NM_145315		108843570	108843570	+1	no_errors	ENST00000368977	ensembl	human	known	69_37n	missense	39	18.75	9	SNP	1.000	A
LLGL2	3993	genome.wustl.edu	37	17	73560440	73560440	+	Silent	SNP	C	C	T			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr17:73560440C>T	ENST00000392550.3	+	10	1005	c.888C>T	c.(886-888)ccC>ccT	p.P296P	LLGL2_ENST00000578363.1_Silent_p.P296P|LLGL2_ENST00000577200.1_Silent_p.P296P|LLGL2_ENST00000375227.4_Silent_p.P296P|LLGL2_ENST00000167462.5_Silent_p.P296P	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	296					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CCAGGTTGCCCTTCACCATCT	0.632																																						dbGAP											0													50.0	44.0	46.0					17																	73560440		2203	4299	6502	-	-	-	SO:0001819	synonymous_variant	0			X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.888C>T	17.37:g.73560440C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14521|Q9BR62	Missense_Mutation	SNP	pfam_LLGL2	p.L14F	ENST00000392550.3	37	c.40	CCDS32733.1	17																																																																																			LLGL2	-	pfam_LLGL2	ENSG00000073350		0.632	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	LLGL2	HGNC	protein_coding	OTTHUMT00000447633.1	149	0.00	0	C	NM_004524		73560440	73560440	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000578638	ensembl	human	known	69_37n	missense	114	13.64	18	SNP	0.980	T
LMNA	4000	genome.wustl.edu	37	1	156108280	156108280	+	Splice_Site	SNP	G	G	T			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr1:156108280G>T	ENST00000368300.4	+	11	1912	c.1700G>T	c.(1699-1701)gGc>gTc	p.G567V	LMNA_ENST00000347559.2_Splice_Site_p.G537V|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000368299.3_Splice_Site_p.G567V|LMNA_ENST00000473598.2_Splice_Site_p.G468V|LMNA_ENST00000448611.2_Splice_Site_p.G455V	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	567	Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					CCTTCCCAGGGCTCCCACTGC	0.706									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																													dbGAP											0													11.0	13.0	12.0					1																	156108280		2171	4258	6429	-	-	-	SO:0001630	splice_region_variant	0	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1699-1G>T	1.37:g.156108280G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Missense_Mutation	SNP	pfam_F,pfam_Lamin_tail_dom,superfamily_Prefoldin	p.G567V	ENST00000368300.4	37	c.1700	CCDS1129.1	1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.366242	0.41902	.	.	ENSG00000160789	ENST00000347559;ENST00000368300;ENST00000368299;ENST00000448611;ENST00000473598;ENST00000508500	D;D;D;D;D;D	0.97888	-4.59;-1.93;-1.99;-1.67;-1.64;-4.59	4.97	4.03	0.46877	.	0.333768	0.25720	N	0.028759	D	0.90642	0.7065	N	0.14661	0.345	0.80722	D	1	P;B;P;P	0.51351	0.829;0.137;0.906;0.944	B;B;B;P	0.44811	0.272;0.084;0.272;0.461	D	0.90956	0.4809	10	0.59425	D	0.04	.	6.6951	0.23195	0.0941:0.182:0.7239:0.0	.	567;468;567;537	Q6UYC3;D6RAQ3;P02545;P02545-3	.;.;LMNA_HUMAN;.	V	537;567;567;455;468;163	ENSP00000292304:G537V;ENSP00000357283:G567V;ENSP00000357282:G567V;ENSP00000395597:G455V;ENSP00000421821:G468V;ENSP00000424977:G163V	ENSP00000292304:G537V	G	+	2	0	LMNA	154374904	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.524000	0.35942	1.252000	0.44001	0.655000	0.94253	GGC	LMNA	-	NULL	ENSG00000160789		0.706	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LMNA	HGNC	protein_coding	OTTHUMT00000039200.2	23	0.00	0	G	NM_170707	Missense_Mutation	156108280	156108280	+1	no_errors	ENST00000368300	ensembl	human	known	69_37n	missense	34	24.44	11	SNP	1.000	T
MPEG1	219972	genome.wustl.edu	37	11	58979531	58979531	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr11:58979531G>A	ENST00000361050.3	-	1	893	c.808C>T	c.(808-810)Cga>Tga	p.R270*	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	270	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.					integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				GAGTTGGTTCGGTTTGAGAGG	0.532																																						dbGAP											0													33.0	31.0	32.0					11																	58979531		1884	4100	5984	-	-	-	SO:0001587	stop_gained	0			AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.808C>T	11.37:g.58979531G>A	ENSP00000354335:p.Arg270*	Somatic		WXS	Illumina GAIIx	Phase_IV	Q2M1T6|Q8TEF8	Nonsense_Mutation	SNP	pfam_MACPF,smart_MACPF	p.R270*	ENST00000361050.3	37	c.808	CCDS41650.1	11	.	.	.	.	.	.	.	.	.	.	G	32	5.177423	0.94846	.	.	ENSG00000197629	ENST00000361050	.	.	.	5.38	2.21	0.28008	.	0.080599	0.50627	D	0.000113	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-7.8646	11.8556	0.52435	0.0:0.0:0.5287:0.4712	.	.	.	.	X	270	.	ENSP00000354335:R270X	R	-	1	2	MPEG1	58736107	1.000000	0.71417	0.977000	0.42913	0.983000	0.72400	1.002000	0.29796	0.609000	0.30018	-0.158000	0.13435	CGA	MPEG1	-	pfam_MACPF,smart_MACPF	ENSG00000197629		0.532	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MPEG1	HGNC	protein_coding	OTTHUMT00000370027.1	102	0.00	0	G	NM_001039396		58979531	58979531	-1	no_errors	ENST00000361050	ensembl	human	known	69_37n	nonsense	106	12.40	15	SNP	0.997	A
PIK3R1	5295	genome.wustl.edu	37	5	67591105	67591107	+	In_Frame_Del	DEL	TAA	TAA	-			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	TAA	TAA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr5:67591105_67591107delTAA	ENST00000521381.1	+	13	2314_2316	c.1698_1700delTAA	c.(1696-1701)attaaa>ata	p.K567del	PIK3R1_ENST00000396611.1_In_Frame_Del_p.K567del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.K204del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.K297del|PIK3R1_ENST00000274335.5_In_Frame_Del_p.K567del|PIK3R1_ENST00000521657.1_In_Frame_Del_p.K567del|PIK3R1_ENST00000320694.8_In_Frame_Del_p.K267del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	567					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.K267_L270delKPDL(1)|p.0?(1)|p.?(1)|p.K297E(1)|p.K567_L570delKPDL(1)|p.K567E(1)|p.K267E(1)|p.K297_L300delKPDL(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TGAACAGCATTAAACCAGACCTT	0.369			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												dbGAP		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	8	Substitution - Missense(3)|Deletion - In frame(3)|Whole gene deletion(1)|Unknown(1)	breast(3)|endometrium(3)|large_intestine(1)|lung(1)																																								-	-	-	SO:0001651	inframe_deletion	0			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1698_1700delTAA	5.37:g.67591105_67591107delTAA	ENSP00000428056:p.Lys567del	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	In_Frame_Del	DEL	pfam_SH2,pfam_RhoGAP_dom,pfam_SH3_2,superfamily_Rho_GTPase_activation_prot,superfamily_SH3_domain,superfamily_Guanylate-bd_C,smart_SH3_domain,smart_RhoGAP_dom,smart_SH2,pfscan_SH2,pfscan_SH3_domain,pfscan_RhoGAP_dom,prints_PI3kinase_P85,prints_SH2	p.K567in_frame_del	ENST00000521381.1	37	c.1698_1700	CCDS3993.1	5																																																																																			PIK3R1	-	prints_PI3kinase_P85	ENSG00000145675		0.369	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIK3R1	HGNC	protein_coding	OTTHUMT00000254013.2	57	0.00	0	TAA	NM_181504		67591105	67591107	+1	no_errors	ENST00000396611	ensembl	human	known	69_37n	in_frame_del	73	17.98	16	DEL	0.993:1.000:1.000	-
PNPLA7	375775	genome.wustl.edu	37	9	140372521	140372521	+	Silent	SNP	G	G	A	rs569684420		TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr9:140372521G>A	ENST00000277531.4	-	24	2958	c.2772C>T	c.(2770-2772)aaC>aaT	p.N924N	PNPLA7_ENST00000492278.1_5'UTR|PNPLA7_ENST00000406427.1_Silent_p.N949N|PNPLA7_ENST00000371457.1_Silent_p.N530N	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	924					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GGGCAATGGCGTTGCCCGTCA	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		16244	0.001		0.0	False		,,,				2504	0.0					dbGAP											0													37.0	25.0	29.0					9																	140372521		2178	4268	6446	-	-	-	SO:0001819	synonymous_variant	0			AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.2772C>T	9.37:g.140372521G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	pfam_cNMP-bd_dom,pfam_Patatin/PLipase_A2-rel,superfamily_Acyl_Trfase/lysoPLipase,superfamily_cNMP-bd-like,smart_cNMP-bd_dom,pfscan_cNMP-bd_dom	p.N949	ENST00000277531.4	37	c.2847	CCDS7045.1	9																																																																																			PNPLA7	-	superfamily_Acyl_Trfase/lysoPLipase	ENSG00000130653		0.662	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	PNPLA7	HGNC	protein_coding	OTTHUMT00000254787.1	118	0.00	0	G	NM_152286		140372521	140372521	-1	no_errors	ENST00000406427	ensembl	human	known	69_37n	silent	123	28.07	48	SNP	0.679	A
POTEI	653269	genome.wustl.edu	37	2	131221170	131221170	+	Missense_Mutation	SNP	C	C	T	rs144934754	byFrequency	TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr2:131221170C>T	ENST00000451531.2	-	15	2877	c.2447G>A	c.(2446-2448)cGc>cAc	p.R816H		NM_001277406.1	NP_001264335.1	P0CG38	POTEI_HUMAN	POTE ankyrin domain family, member I	816	Actin-like.				retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				lung(11)	11						CATCTTCTCGCGGTTGGCCTT	0.597													c|||	4225	0.84365	0.6256	0.9164	5008	,	,		15382	0.9831		0.9006	False		,,,				2504	0.8845					dbGAP											0																																										-	-	-	SO:0001583	missense	0				CCDS59431.1	2q21.1	2013-01-10			ENSG00000196834	ENSG00000196834		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37093	protein-coding gene	gene with protein product						16364570	Standard	NM_001277406		Approved	POTE2beta	uc031rpa.1	P0CG38	OTTHUMG00000153925	ENST00000451531.2:c.2447G>A	2.37:g.131221170C>T	ENSP00000392718:p.Arg816His	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Actin-like,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Actin-like,prints_Actin-like,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.R816H	ENST00000451531.2	37	c.2447	CCDS59431.1	2	.	.	.	.	.	.	.	.	.	.	.	16.92	3.256235	0.59321	.	.	ENSG00000196834	ENST00000451531	D	0.97066	-4.23	.	.	.	.	.	.	.	.	D	0.98865	0.9616	H	0.99668	4.69	0.43175	P	0.005017999999999967	.	.	.	.	.	.	D	0.97102	0.9798	5	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	.	.	.	H	816	ENSP00000392718:R816H	ENSP00000392718:R816H	R	-	2	0	POTEI	130937640	1.000000	0.71417	0.195000	0.23364	0.197000	0.23852	5.220000	0.65267	0.119000	0.18210	0.121000	0.15741	CGC	POTEI	-	pfam_Actin-like,smart_Actin-like,prints_Actin-like	ENSG00000196834		0.597	POTEI-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	POTEI	HGNC	protein_coding	OTTHUMT00000333222.2	26	0.00	0	C	XM_928585		131221170	131221170	-1	no_errors	ENST00000451531	ensembl	human	novel	69_37n	missense	21	16.00	4	SNP	1.000	T
SIPA1L1	26037	genome.wustl.edu	37	14	72138262	72138262	+	Silent	SNP	C	C	T			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr14:72138262C>T	ENST00000555818.1	+	8	3030	c.2682C>T	c.(2680-2682)agC>agT	p.S894S	SIPA1L1_ENST00000358550.2_Silent_p.S894S|SIPA1L1_ENST00000381232.3_Silent_p.S894S|SIPA1L1_ENST00000537413.1_Silent_p.S369S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	894					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.S894S(2)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		AAACAAAGAGCGTGGTCTTCA	0.463																																						dbGAP											2	Substitution - coding silent(2)	lung(2)											133.0	127.0	129.0					14																	72138262		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.2682C>T	14.37:g.72138262C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	pfam_DUF3401,pfam_Rap_GAP,pfam_PDZ,superfamily_PDZ,smart_PDZ,pfscan_PDZ,pfscan_Rap_GAP	p.S894	ENST00000555818.1	37	c.2682	CCDS9807.1	14																																																																																			SIPA1L1	-	NULL	ENSG00000197555		0.463	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SIPA1L1	HGNC	protein_coding	OTTHUMT00000412806.1	44	0.00	0	C	NM_015556		72138262	72138262	+1	no_errors	ENST00000555818	ensembl	human	known	69_37n	silent	65	21.69	18	SNP	0.139	T
SNORD3B-1	26851	genome.wustl.edu	37	17	18965270	18965271	+	lincRNA	INS	-	-	T			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr17:18965270_18965271insT	ENST00000363359.1	+	0	46_47				SNORD3B-2_ENST00000364880.1_lincRNA					small nucleolar RNA, C/D box 3B-1																		ttactagagaagtttctctgaa	0.49																																						dbGAP											0																																										-	-	-			0			AF020534, AF020533, AF020532		17p11.2	2013-09-05	2006-11-28	2006-11-28	ENSG00000200229	ENSG00000265185			10168	non-coding RNA	RNA, small nucleolar			"""RNA, U3A1 small nucleolar, RNA, U3A1 small nucleolar"""	RNU3A1		9365252	Standard	NR_003271		Approved	U3a, U3b1, U3b2					17.37:g.18965270_18965271insT		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	INS	-	NULL	ENST00000363359.1	37	NULL		17																																																																																			SNORD3B-1	-	-	ENSG00000200229		0.490	SNORD3B-1-201	KNOWN	basic	snoRNA	SNORD3B-1	HGNC	lincRNA		19	0.00	0	-	NR_003271		18965270	18965271	+1	no_errors	ENST00000363359	ensembl	human	known	69_37n	rna	16	27.27	6	INS	0.096:0.102	T
STAG1	10274	genome.wustl.edu	37	3	136170958	136170958	+	Missense_Mutation	SNP	C	C	G			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr3:136170958C>G	ENST00000383202.2	-	14	1601	c.1345G>C	c.(1345-1347)Gaa>Caa	p.E449Q	STAG1_ENST00000236698.5_Missense_Mutation_p.E449Q|STAG1_ENST00000434713.2_Missense_Mutation_p.E223Q|STAG1_ENST00000536929.1_Missense_Mutation_p.E33Q	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	449					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						GCTAATGCTTCTTCTGCTTGT	0.393																																						dbGAP											0													127.0	113.0	118.0					3																	136170958		2203	4300	6503	-	-	-	SO:0001583	missense	0			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.1345G>C	3.37:g.136170958C>G	ENSP00000372689:p.Glu449Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	O00539|Q6P275	Missense_Mutation	SNP	pfam_STAG,superfamily_ARM-type_fold	p.E449Q	ENST00000383202.2	37	c.1345	CCDS3090.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.4|23.4	4.412296|4.412296	0.83340|0.83340	.|.	.|.	ENSG00000118007|ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929|ENST00000492318	T;T;T;T|.	0.32988|.	1.82;1.83;1.85;1.43|.	5.51|5.51	5.51|5.51	0.81932|0.81932	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60379|0.60379	0.2264|0.2264	L|L	0.33485|0.33485	1.01|1.01	0.80722|0.80722	D|D	1|1	B;B;B|.	0.19706|.	0.005;0.038;0.005|.	B;B;B|.	0.18561|.	0.005;0.022;0.009|.	T|T	0.54146|0.54146	-0.8337|-0.8337	10|5	0.24483|.	T|.	0.36|.	.|.	19.4087|19.4087	0.94660|0.94660	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	466;449;449|.	Q4LE48;Q6P275;Q8WVM7|.	.;.;STAG1_HUMAN|.	Q|N	449;449;223;33|59	ENSP00000372689:E449Q;ENSP00000236698:E449Q;ENSP00000404396:E223Q;ENSP00000445787:E33Q|.	ENSP00000236698:E449Q|.	E|K	-|-	1|3	0|2	STAG1|STAG1	137653648|137653648	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.818000|7.818000	0.86416|0.86416	2.588000|2.588000	0.87417|0.87417	0.591000|0.591000	0.81541|0.81541	GAA|AAG	STAG1	-	superfamily_ARM-type_fold	ENSG00000118007		0.393	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STAG1	HGNC	protein_coding	OTTHUMT00000357366.1	187	0.53	1	C	NM_005862		136170958	136170958	-1	no_errors	ENST00000383202	ensembl	human	known	69_37n	missense	151	20.94	40	SNP	1.000	G
SUCLG1	8802	genome.wustl.edu	37	2	84650707	84650707	+	3'UTR	SNP	A	A	G	rs2832	byFrequency	TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr2:84650707A>G	ENST00000393868.2	-	0	1414				SUCLG1_ENST00000491123.1_5'UTR	NM_003849.3	NP_003840.2	P53597	SUCA_HUMAN	succinate-CoA ligase, alpha subunit						cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			kidney(4)|large_intestine(4)|lung(2)	10					Succinic acid(DB00139)	TGGTGAAAACATCTTAATTCA	0.393													A|||	4017	0.802117	0.4667	0.9092	5008	,	,		18229	0.9246		0.9374	False		,,,				2504	0.9141				Ovarian(48;203 1101 37206 40305 50790)	dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			Z68204	CCDS1967.2	2p11.3	2008-02-05	2008-01-08		ENSG00000163541	ENSG00000163541	6.2.1.4		11449	protein-coding gene	gene with protein product		611224	"""succinate-CoA ligase, GDP-forming, alpha subunit"""			9128182	Standard	NM_003849		Approved		uc002son.3	P53597	OTTHUMG00000130023	ENST00000393868.2:c.*163T>C	2.37:g.84650707A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9BWB0|Q9UNP6	RNA	SNP	-	NULL	ENST00000393868.2	37	NULL	CCDS1967.2	2																																																																																			SUCLG1	-	-	ENSG00000163541		0.393	SUCLG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SUCLG1	HGNC	protein_coding	OTTHUMT00000252298.2	22	0.00	0	A	NM_003849		84650707	84650707	-1	no_errors	ENST00000491123	ensembl	human	known	69_37n	rna	37	13.95	6	SNP	0.007	G
TARS2	80222	genome.wustl.edu	37	1	150479466	150479466	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr1:150479466G>A	ENST00000369064.3	+	18	2117	c.2083G>A	c.(2083-2085)Gac>Aac	p.D695N	ECM1_ENST00000369047.4_5'Flank|ECM1_ENST00000369049.4_5'Flank|ECM1_ENST00000346569.6_5'Flank|TARS2_ENST00000606933.1_Missense_Mutation_p.D613N|TARS2_ENST00000369054.2_Missense_Mutation_p.D565N	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	695					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	TGGGGAGTGGGACTTGCCTGA	0.502																																						dbGAP											0													108.0	101.0	103.0					1																	150479466		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.2083G>A	1.37:g.150479466G>A	ENSP00000358060:p.Asp695Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	pfam_aa-tRNA-synt_IIb_cons-dom,pfam_Anticodon-bd,pfam_TGS,pfam_tRNA_SAD,superfamily_Thr/Ala-tRNA-synth_IIc_edit,superfamily_Anticodon-bd,superfamily_TGS-like,smart_tRNA_SAD,pfscan_aa-tRNA-synth_II,prints_Thr-tRNA-synth_IIa,tigrfam_Thr-tRNA-synth_IIa	p.D695N	ENST00000369064.3	37	c.2083	CCDS952.1	1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.506278	0.44558	.	.	ENSG00000143374	ENST00000369054;ENST00000369064;ENST00000369051;ENST00000369052	D;D;D	0.82526	-1.62;-1.62;-1.62	5.26	2.01	0.26516	Anticodon-binding (3);	0.704592	0.13941	N	0.352168	T	0.60457	0.2270	L	0.34521	1.04	0.09310	N	1	P;B;B	0.44344	0.833;0.237;0.43	B;B;B	0.43508	0.422;0.079;0.175	T	0.50767	-0.8789	10	0.41790	T	0.15	-36.3754	6.9963	0.24784	0.1762:0.1373:0.6866:0.0	.	565;420;695	Q9H9V2;E7EVR9;Q9BW92	.;.;SYTM_HUMAN	N	565;695;420;420	ENSP00000358050:D565N;ENSP00000358060:D695N;ENSP00000358047:D420N	ENSP00000358047:D420N	D	+	1	0	TARS2	148746090	0.000000	0.05858	0.004000	0.12327	0.001000	0.01503	0.251000	0.18257	0.677000	0.31305	-0.137000	0.14449	GAC	TARS2	-	pfam_Anticodon-bd,superfamily_Anticodon-bd,tigrfam_Thr-tRNA-synth_IIa	ENSG00000143374		0.502	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TARS2	HGNC	protein_coding	OTTHUMT00000035847.1	51	0.00	0	G	NM_025150		150479466	150479466	+1	no_errors	ENST00000369064	ensembl	human	known	69_37n	missense	40	31.03	18	SNP	0.003	A
TBC1D29	26083	genome.wustl.edu	37	17	28890301	28890301	+	Missense_Mutation	SNP	G	G	A	rs80145926	byFrequency	TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr17:28890301G>A	ENST00000580161.1	+	6	2808	c.311G>A	c.(310-312)aGc>aAc	p.S104N	TBC1D29_ENST00000584297.1_3'UTR|RP11-218M11.1_ENST00000563063.1_lincRNA|TBC1D29_ENST00000579181.1_Missense_Mutation_p.S104N			Q9UFV1	TBC29_HUMAN	TBC1 domain family, member 29	104							Rab GTPase activator activity (GO:0005097)	p.S104N(1)		breast(1)|kidney(1)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Myeloproliferative disorder(56;0.0255)				TCAGAGAGCAGCAGAGGCCCC	0.587																																						dbGAP											1	Substitution - Missense(1)	prostate(1)											48.0	45.0	46.0					17																	28890301		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC096718	CCDS32606.1	17q11.2	2014-09-04			ENSG00000266733	ENSG00000266733			24509	protein-coding gene	gene with protein product						12618308	Standard	XM_006721805		Approved	DKFZP434O047	uc002hfh.3	Q9UFV1	OTTHUMG00000178857	ENST00000580161.1:c.311G>A	17.37:g.28890301G>A	ENSP00000462799:p.Ser104Asn	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	superfamily_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	p.S104N	ENST00000580161.1	37	c.311	CCDS32606.1	17	.	.	.	.	.	.	.	.	.	.	.	9.179	1.023040	0.19433	.	.	ENSG00000197689	ENST00000329040	.	.	.	.	.	.	.	.	.	.	.	T	0.22820	0.0551	N	0.08118	0	0.18873	N	0.999983	B	0.33000	0.393	B	0.42319	0.383	T	0.34850	-0.9812	7	0.72032	D	0.01	.	5.89	0.18904	8.0E-4:0.0:0.9992:0.0	.	104	Q9UFV1	TBC29_HUMAN	N	104	.	ENSP00000330052:S104N	S	+	2	0	TBC1D29	25914427	0.966000	0.33281	0.071000	0.20095	0.071000	0.16799	-0.367000	0.07553	0.107000	0.17824	0.109000	0.15622	AGC	TBC1D29	-	NULL	ENSG00000266733		0.587	TBC1D29-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	TBC1D29	HGNC	protein_coding	OTTHUMT00000443632.1	43	0.00	0	G	NM_015594		28890301	28890301	+1	no_errors	ENST00000579181	ensembl	human	known	69_37n	missense	60	14.29	10	SNP	0.904	A
TPRX1	284355	genome.wustl.edu	37	19	48305634	48305634	+	Missense_Mutation	SNP	A	A	G	rs372678982|rs201640420		TCGA-A2-A4RX-01A-11D-A25Q-09	TCGA-A2-A4RX-10A-01D-A25Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	056e8bbf-115e-4226-b2c3-fec4a965f01f	8e67ed48-58b5-403c-8e4c-d0a3fbd299bc	g.chr19:48305634A>G	ENST00000322175.3	-	2	789	c.634T>C	c.(634-636)Tca>Cca	p.S212P	TPRX1_ENST00000543508.1_Missense_Mutation_p.S202P|TPRX1_ENST00000535759.1_Missense_Mutation_p.S309P	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	212	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		attgggcctgagattgggcct	0.667																																					Esophageal Squamous(123;175 2281 3051 32395)	dbGAP											0													13.0	10.0	11.0					19																	48305634		1838	3561	5399	-	-	-	SO:0001583	missense	0				CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.634T>C	19.37:g.48305634A>G	ENSP00000323455:p.Ser212Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	A5D8Y3|B2RPL5	Missense_Mutation	SNP	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain	p.S309P	ENST00000322175.3	37	c.925	CCDS33066.1	19	.	.	.	.	.	.	.	.	.	.	-	2.272	-0.366679	0.05069	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.19250	2.16;2.16;2.16	0.365	-0.73	0.11154	.	.	.	.	.	T	0.05456	0.0144	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31024	-0.9958	8	0.02654	T	1	.	.	.	.	.	212	Q8N7U7	TPRX1_HUMAN	P	212;309;202	ENSP00000323455:S212P;ENSP00000438832:S309P;ENSP00000438712:S202P	ENSP00000323455:S212P	S	-	1	0	TPRX1	52997446	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.480000	0.06559	-2.213000	0.00735	-2.237000	0.00289	TCA	TPRX1	-	NULL	ENSG00000178928		0.667	TPRX1-001	KNOWN	basic|CCDS	protein_coding	TPRX1	HGNC	protein_coding	OTTHUMT00000409868.1	133	0.75	1	A	NM_198479		48305634	48305634	-1	no_errors	ENST00000535759	ensembl	human	known	69_37n	missense	182	11.59	24	SNP	0.000	G
