#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
ATP2B1	490	genome.wustl.edu	37	12	90018057	90018057	+	Missense_Mutation	SNP	A	A	C			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr12:90018057A>C	ENST00000428670.3	-	9	1703	c.1247T>G	c.(1246-1248)tTt>tGt	p.F416C	ATP2B1_ENST00000261173.2_Missense_Mutation_p.F416C|ATP2B1_ENST00000359142.3_Missense_Mutation_p.F416C|ATP2B1_ENST00000393164.2_Missense_Mutation_p.F159C|ATP2B1_ENST00000348959.3_Missense_Mutation_p.F416C			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	416					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						GAACTTCACAAAGTATTGTAT	0.388																																						dbGAP											0													81.0	75.0	77.0					12																	90018057		2203	4300	6503	-	-	-	SO:0001583	missense	0			J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1247T>G	12.37:g.90018057A>C	ENSP00000392043:p.Phe416Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Missense_Mutation	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_ATPase_P-typ_cation-transptr_C,pfam_ATP_Ca_trans_C,pfam_Dehalogen-like_hydro,pfam_ATPase_P-typ_cation-transptr_N,pfam_HAD-SF_hydro-like_3,superfamily_ATPase_cation_domN,superfamily_HAD-like_dom,smart_ATPase_P-typ_cation-transptr_N,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Ca-transp_PMCA,tigrfam_ATPase_P-typ_ion-transptr	p.F416C	ENST00000428670.3	37	c.1247	CCDS9035.1	12	.	.	.	.	.	.	.	.	.	.	A	23.9	4.475492	0.84640	.	.	ENSG00000070961	ENST00000261173;ENST00000348959;ENST00000359142;ENST00000428670;ENST00000393164	D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.44	5.55	5.55	0.83447	.	0.047279	0.85682	D	0.000000	D	0.96374	0.8817	M	0.93283	3.4	0.80722	D	1	D;D;D	0.71674	0.969;0.998;0.973	P;D;P	0.68192	0.724;0.956;0.907	D	0.97409	1.0001	9	.	.	.	-22.0472	15.6842	0.77396	1.0:0.0:0.0:0.0	.	416;416;416	P20020-3;P20020-2;P20020-6	.;.;.	C	416;416;416;416;159	ENSP00000261173:F416C;ENSP00000343599:F416C;ENSP00000352054:F416C;ENSP00000392043:F416C;ENSP00000376869:F159C	.	F	-	2	0	ATP2B1	88542188	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	9.339000	0.96797	2.110000	0.64415	0.482000	0.46254	TTT	ATP2B1	-	pfam_ATPase_P-typ_ATPase-assoc-dom,tigrfam_ATPase_P-typ_Ca-transp_PMCA,tigrfam_ATPase_P-typ_ion-transptr	ENSG00000070961		0.388	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	ATP2B1	HGNC	protein_coding	OTTHUMT00000406653.1	122	0.00	0	A	NM_001682		90018057	90018057	-1	no_errors	ENST00000261173	ensembl	human	known	69_37n	missense	89	13.59	14	SNP	1.000	C
CDH11	1009	genome.wustl.edu	37	16	65016151	65016151	+	Silent	SNP	G	G	A	rs201295294	byFrequency	TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr16:65016151G>A	ENST00000268603.4	-	8	1668	c.1053C>T	c.(1051-1053)aaC>aaT	p.N351N	CDH11_ENST00000394156.3_Silent_p.N351N|CDH11_ENST00000566827.1_Silent_p.N225N	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	351	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CGATGTGCACGTTGGCTGCCT	0.453			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	2	0.000399361	0.0	0.0	5008	,	,		18178	0.002		0.0	False		,,,				2504	0.0					dbGAP		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	0													117.0	94.0	102.0					16																	65016151		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1053C>T	16.37:g.65016151G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.N351	ENST00000268603.4	37	c.1053	CCDS10803.1	16																																																																																			CDH11	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	ENSG00000140937		0.453	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH11	HGNC	protein_coding	OTTHUMT00000268755.1	112	0.00	0	G	NM_033664		65016151	65016151	-1	no_errors	ENST00000268603	ensembl	human	known	69_37n	silent	108	12.90	16	SNP	0.962	A
CHI3L1	1116	genome.wustl.edu	37	1	203154335	203154335	+	Silent	SNP	G	G	C			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr1:203154335G>C	ENST00000255409.3	-	3	359	c.234C>G	c.(232-234)ggC>ggG	p.G78G		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	78					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						TGTTGAGCATGCCGTAGAGCG	0.582																																						dbGAP											0													133.0	125.0	128.0					1																	203154335		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.234C>G	1.37:g.203154335G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R7B0|P30923|Q8IVA4|Q96HI7	Silent	SNP	pfam_Glyco_hydro18cat,superfamily_Glycoside_hydrolase_SF,smart_Chitinase_II	p.G78	ENST00000255409.3	37	c.234	CCDS1435.1	1																																																																																			CHI3L1	-	pfam_Glyco_hydro18cat,superfamily_Glycoside_hydrolase_SF,smart_Chitinase_II	ENSG00000133048		0.582	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHI3L1	HGNC	protein_coding	OTTHUMT00000100265.1	82	0.00	0	G	NM_001276		203154335	203154335	-1	no_errors	ENST00000255409	ensembl	human	known	69_37n	silent	89	29.37	37	SNP	0.016	C
FAT3	120114	genome.wustl.edu	37	11	92533820	92533820	+	Missense_Mutation	SNP	C	C	G			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr11:92533820C>G	ENST00000298047.6	+	9	7658	c.7641C>G	c.(7639-7641)gaC>gaG	p.D2547E	FAT3_ENST00000525166.1_Missense_Mutation_p.D2397E|FAT3_ENST00000409404.2_Missense_Mutation_p.D2547E			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2547	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCCTCATAGACAGCAATGGGC	0.488										TCGA Ovarian(4;0.039)																												dbGAP											0													47.0	47.0	47.0					11																	92533820		2036	4182	6218	-	-	-	SO:0001583	missense	0			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.7641C>G	11.37:g.92533820C>G	ENSP00000298047:p.Asp2547Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	B5MDB0|Q96AU6	Missense_Mutation	SNP	pfam_Cadherin,pfam_Laminin_G,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl,superfamily_Cadherin-like,smart_Cadherin,smart_EGF-like,smart_Laminin_G,smart_EGF-like_Ca-bd,prints_Cadherin,pfscan_EG-like_dom,pfscan_Laminin_G,pfscan_Cadherin	p.D2547E	ENST00000298047.6	37	c.7641		11	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843945	0.51164	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.64260	-0.09;-0.09;-0.09	5.95	3.07	0.35406	.	.	.	.	.	T	0.75686	0.3883	M	0.77616	2.38	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.73880	-0.3843	9	0.56958	D	0.05	.	8.5703	0.33565	0.0:0.6254:0.0:0.3746	.	2547	Q8TDW7-3	.	E	2547;2547;2397	ENSP00000298047:D2547E;ENSP00000387040:D2547E;ENSP00000432586:D2397E	ENSP00000298047:D2547E	D	+	3	2	FAT3	92173468	0.865000	0.29922	0.992000	0.48379	0.911000	0.54048	0.704000	0.25661	0.398000	0.25338	0.655000	0.94253	GAC	FAT3	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000165323		0.488	FAT3-201	KNOWN	basic	protein_coding	FAT3	HGNC	protein_coding		109	0.00	0	C	NM_001008781		92533820	92533820	+1	no_errors	ENST00000298047	ensembl	human	known	69_37n	missense	96	26.72	35	SNP	0.576	G
HLF	3131	genome.wustl.edu	37	17	53345424	53345424	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr17:53345424G>A	ENST00000226067.5	+	2	901	c.428G>A	c.(427-429)tGt>tAt	p.C143Y	HLF_ENST00000575345.1_Missense_Mutation_p.C58Y|HLF_ENST00000573945.1_Missense_Mutation_p.C58Y|HLF_ENST00000430986.2_Missense_Mutation_p.C58Y	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	143					multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(2)	3						TCTCCGAACTGTATGCAGAGC	0.597			T	TCF3	ALL																																	dbGAP		Dom	yes		17	17q22	3131	hepatic leukemia factor		L	0													58.0	59.0	59.0					17																	53345424		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.428G>A	17.37:g.53345424G>A	ENSP00000226067:p.Cys143Tyr	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1X8|Q6FHS9	Missense_Mutation	SNP	pfam_bZIP_2,smart_bZIP,pfscan_bZIP	p.C143Y	ENST00000226067.5	37	c.428	CCDS11585.1	17	.	.	.	.	.	.	.	.	.	.	G	26.3	4.724389	0.89298	.	.	ENSG00000108924	ENST00000226067;ENST00000430986	.	.	.	5.94	5.94	0.96194	.	0.136296	0.52532	D	0.000066	T	0.57007	0.2024	M	0.71581	2.175	0.80722	D	1	P	0.44877	0.845	B	0.41723	0.365	T	0.59144	-0.7509	9	0.02654	T	1	.	19.3401	0.94337	0.0:0.0:1.0:0.0	.	143	Q16534	HLF_HUMAN	Y	143;58	.	ENSP00000226067:C143Y	C	+	2	0	HLF	50700423	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	7.632000	0.83247	2.803000	0.96430	0.655000	0.94253	TGT	HLF	-	NULL	ENSG00000108924		0.597	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HLF	HGNC	protein_coding	OTTHUMT00000439185.1	58	0.00	0	G	NM_002126		53345424	53345424	+1	no_errors	ENST00000226067	ensembl	human	known	69_37n	missense	33	61.18	52	SNP	1.000	A
Unknown	0	genome.wustl.edu	37	3	195345561	195345561	+	IGR	SNP	A	A	G			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr3:195345561A>G								APOD (34485 upstream) : RP11-141C7.4 (21299 downstream)																							GCCCGCTATGACTCTAGCACC	0.607																																						dbGAP											0																																										-	-	-	SO:0001628	intergenic_variant	0																															3.37:g.195345561A>G		Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	NULL	p.T12A		37	c.34		3	.	.	.	.	.	.	.	.	.	.	.	10.95	1.496118	0.26774	.	.	ENSG00000176945	ENST00000381954	.	.	.	0.682	0.682	0.17992	.	.	.	.	.	T	0.38506	0.1043	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34329	-0.9833	4	0.52906	T	0.07	.	.	.	.	.	.	.	.	A	12	.	ENSP00000371380:T12A	T	+	1	0	MUC20	196826850	0.089000	0.21612	0.006000	0.13384	0.005000	0.04900	1.745000	0.38278	0.556000	0.29098	0.331000	0.21540	ACT	MUC20	-	NULL	ENSG00000176945	0	0.607					MUC20	HGNC			8	0.00	0	A			195345561	195345561	+1	no_errors	ENST00000381954	ensembl	human	known	69_37n	missense	1	80.00	4	SNP	0.007	G
NEDD4	4734	genome.wustl.edu	37	15	56141078	56141078	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr15:56141078G>A	ENST00000508342.1	-	11	2910	c.2611C>T	c.(2611-2613)Cca>Tca	p.P871S	NEDD4_ENST00000435532.3_Missense_Mutation_p.P452S|NEDD4_ENST00000506154.1_Missense_Mutation_p.P855S|NEDD4_ENST00000338963.2_Missense_Mutation_p.P799S	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	871	Mediates interaction with TNIK. {ECO:0000250}.|WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		TTCAATCTTGGATCTTCCTTT	0.333																																						dbGAP											0													147.0	136.0	140.0					15																	56141078		2193	4292	6485	-	-	-	SO:0001583	missense	0			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.2611C>T	15.37:g.56141078G>A	ENSP00000424827:p.Pro871Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	pfam_HECT,pfam_WW_Rsp5_WWP,superfamily_HECT,superfamily_WW_Rsp5_WWP,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_WW_Rsp5_WWP,smart_HECT,pfscan_HECT,pfscan_WW_Rsp5_WWP	p.P871S	ENST00000508342.1	37	c.2611		15	.	.	.	.	.	.	.	.	.	.	G	21.9	4.209500	0.79240	.	.	ENSG00000069869	ENST00000508342;ENST00000435532;ENST00000338963;ENST00000506154	D;D;D;D	0.99382	-5.8;-5.8;-5.8;-5.8	5.41	5.41	0.78517	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	D	0.99579	0.9848	M	0.93638	3.44	0.80722	D	1	P;D;D;D	0.69078	0.734;0.997;0.975;0.969	P;D;D;D	0.75484	0.519;0.986;0.966;0.943	D	0.98078	1.0402	10	0.87932	D	0	.	18.1848	0.89789	0.0:0.0:1.0:0.0	.	855;452;871;799	P46934-2;P46934-4;P46934;P46934-3	.;.;NEDD4_HUMAN;.	S	871;452;799;855	ENSP00000424827:P871S;ENSP00000410613:P452S;ENSP00000345530:P799S;ENSP00000422705:P855S	ENSP00000345530:P799S	P	-	1	0	NEDD4	53928370	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.999000	0.76283	2.530000	0.85305	0.655000	0.94253	CCA	NEDD4	-	pfam_WW_Rsp5_WWP,superfamily_WW_Rsp5_WWP,smart_WW_Rsp5_WWP,pfscan_WW_Rsp5_WWP	ENSG00000069869		0.333	NEDD4-002	KNOWN	basic	protein_coding	NEDD4	HGNC	protein_coding	OTTHUMT00000359817.1	327	0.00	0	G	NM_198400		56141078	56141078	-1	no_errors	ENST00000508342	ensembl	human	known	69_37n	missense	246	17.67	53	SNP	1.000	A
PHIP	55023	genome.wustl.edu	37	6	79665349	79665351	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	TTC	TTC					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr6:79665349_79665351delTTC	ENST00000275034.4	-	33	3998_4000	c.3831_3833delGAA	c.(3829-3834)aagaaa>aaa	p.1277_1278KK>K	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1277					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AGACAAAACTTTCTTCTTCATTG	0.246																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.3831_3833delGAA	6.37:g.79665355_79665357delTTC	ENSP00000275034:p.Lys1278del	Somatic		WXS	Illumina GAIIx	Phase_IV	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	In_Frame_Del	DEL	pfam_WD40_repeat,pfam_Bromodomain,superfamily_Quinonprotein_ADH-like,superfamily_Bromodomain,smart_WD40_repeat,smart_Bromodomain,pfscan_Bromodomain,pfscan_WD40_repeat,pfscan_WD40_repeat_dom,prints_Bromodomain	p.K1278in_frame_del	ENST00000275034.4	37	c.3833_3831	CCDS4987.1	6																																																																																			PHIP	-	NULL	ENSG00000146247		0.246	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHIP	HGNC	protein_coding	OTTHUMT00000041297.2	171	0.00	0	TTC			79665349	79665351	-1	no_errors	ENST00000275034	ensembl	human	known	69_37n	in_frame_del	75	12.64	11	DEL	1.000:1.000:1.000	-
PNLIP	5406	genome.wustl.edu	37	10	118318677	118318677	+	Silent	SNP	C	C	T			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr10:118318677C>T	ENST00000369221.2	+	10	970	c.942C>T	c.(940-942)ttC>ttT	p.F314F		NM_000936.2	NP_000927.1	P16233	LIPP_HUMAN	pancreatic lipase	314					intestinal cholesterol absorption (GO:0030299)|lipid catabolic process (GO:0016042)|lipid digestion (GO:0044241)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|triglyceride lipase activity (GO:0004806)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	43				all cancers(201;0.0131)	Glycerol Phenylbutyrate(DB08909)|Orlistat(DB01083)	ACAAGTGTTTCCCTTGTCCAA	0.408																																						dbGAP											0													102.0	89.0	93.0					10																	118318677		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC014309	CCDS7594.1	10q25.3	2012-07-31			ENSG00000175535	ENSG00000175535	3.1.1.3		9155	protein-coding gene	gene with protein product		246600				1783385	Standard	NM_000936		Approved	PL	uc001lcm.3	P16233	OTTHUMG00000019103	ENST00000369221.2:c.942C>T	10.37:g.118318677C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VSQ2	Silent	SNP	pfam_Lipase_N,pfam_LipOase_LH2,superfamily_Lipase_LipOase,smart_LipOase_LH2,pirsf_Lipoprotein_lipase_LIPH,pfscan_LipOase_LH2,prints_Lipase,prints_Lipase_panc	p.F314	ENST00000369221.2	37	c.942	CCDS7594.1	10																																																																																			PNLIP	-	pfam_Lipase_N,pirsf_Lipoprotein_lipase_LIPH,prints_Lipase	ENSG00000175535		0.408	PNLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PNLIP	HGNC	protein_coding	OTTHUMT00000050524.1	230	0.00	0	C	NM_000936		118318677	118318677	+1	no_errors	ENST00000369221	ensembl	human	known	69_37n	silent	131	18.12	29	SNP	1.000	T
PTPN13	5783	genome.wustl.edu	37	4	87728895	87728895	+	Missense_Mutation	SNP	C	C	G			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr4:87728895C>G	ENST00000411767.2	+	45	6991	c.6928C>G	c.(6928-6930)Caa>Gaa	p.Q2310E	PTPN13_ENST00000436978.1_Missense_Mutation_p.Q2315E|PTPN13_ENST00000316707.6_Missense_Mutation_p.Q2119E|PTPN13_ENST00000427191.2_Missense_Mutation_p.Q2291E|PTPN13_ENST00000511467.1_Missense_Mutation_p.Q2315E			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2310	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CATGATGACTCAAGAAGTAGA	0.463																																						dbGAP											0													151.0	144.0	146.0					4																	87728895		1922	4123	6045	-	-	-	SO:0001583	missense	0				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.6928C>G	4.37:g.87728895C>G	ENSP00000407249:p.Gln2310Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	pirsf_Tyr_Pase_non-rcpt_typ-13,pfam_Tyr_Pase_rcpt/non-rcpt,pfam_PDZ,pfam_FERM_central,pfam_FERM_PH-like_C,pfam_FERM_N,superfamily_FERM_central,superfamily_PDZ,superfamily_PAZ,smart_KIND,smart_Band_41_domain,smart_PDZ,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,prints_Tyr_Pase_rcpt/non-rcpt,prints_Band_41_fam,pfscan_FERM_domain,pfscan_PDZ,pfscan_Tyr/Dual-specificity_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt	p.Q2315E	ENST00000411767.2	37	c.6943	CCDS47094.1	4	.	.	.	.	.	.	.	.	.	.	C	28.5	4.928714	0.92389	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66	5.68	5.68	0.88126	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.139487	0.32624	N	0.005851	T	0.24547	0.0595	L	0.29908	0.895	0.51233	D	0.99991	B;P;D;D	0.54964	0.434;0.934;0.969;0.962	B;P;P;P	0.57324	0.213;0.674;0.818;0.722	T	0.00397	-1.1765	10	0.54805	T	0.06	.	19.8003	0.96504	0.0:1.0:0.0:0.0	.	2119;2291;2310;2315	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	E	2291;2315;2119;2310;2315;2259	ENSP00000408368:Q2291E;ENSP00000394794:Q2315E;ENSP00000322675:Q2119E;ENSP00000407249:Q2310E;ENSP00000426626:Q2315E	ENSP00000322675:Q2119E	Q	+	1	0	PTPN13	87947919	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.666000	0.83877	2.672000	0.90937	0.650000	0.86243	CAA	PTPN13	-	pirsf_Tyr_Pase_non-rcpt_typ-13,pfam_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_rcpt/non-rcpt,pfscan_Tyr_Pase_rcpt/non-rcpt	ENSG00000163629		0.463	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	PTPN13	HGNC	protein_coding	OTTHUMT00000363191.1	147	0.00	0	C			87728895	87728895	+1	no_errors	ENST00000436978	ensembl	human	known	69_37n	missense	120	11.11	15	SNP	1.000	G
TRIM74	378108	genome.wustl.edu	37	7	72436307	72436307	+	Missense_Mutation	SNP	C	C	T	rs3852229		TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr7:72436307C>T	ENST00000285805.3	-	2	581	c.382G>A	c.(382-384)Gtc>Atc	p.V128I	TRIM74_ENST00000395244.1_Missense_Mutation_p.V128I	NM_198853.1	NP_942150.1	Q86UV6	TRI74_HUMAN	tripartite motif containing 74	128				V -> I (in Ref. 3; AAH33871). {ECO:0000305}.		intracellular (GO:0005622)	zinc ion binding (GO:0008270)			prostate(1)	1						CGGCTGCAGACGGTGGAGACG	0.672																																						dbGAP											0													3.0	3.0	3.0					7																	72436307		847	2073	2920	-	-	-	SO:0001583	missense	0			AF498999	CCDS5545.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000155428	ENSG00000155428		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	17453	protein-coding gene	gene with protein product		612550	"""tripartite motif-containing 50C"", ""tripartite motif-containing 74"""	TRIM50C			Standard	NM_198853		Approved	MGC45440		Q86UV6	OTTHUMG00000129851	ENST00000285805.3:c.382G>A	7.37:g.72436307C>T	ENSP00000285805:p.Val128Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B7WP46	Missense_Mutation	SNP	pfam_Znf_B-box,pfam_Znf_C3HC4_RING-type,smart_Znf_RING,smart_Znf_B-box,pfscan_Znf_B-box,pfscan_Znf_RING	p.V128I	ENST00000285805.3	37	c.382	CCDS5545.1	7	.	.	.	.	.	.	.	.	.	.	C	10.31	1.315663	0.23908	.	.	ENSG00000155428	ENST00000395244;ENST00000285805	T;T	0.57107	0.42;0.42	1.93	1.93	0.25924	.	0.119478	0.36519	N	0.002554	T	0.37376	0.1001	N	0.24115	0.695	0.23351	N	0.997853	D	0.53462	0.96	B	0.43225	0.412	T	0.31251	-0.9950	10	0.46703	T	0.11	.	11.4209	0.49980	0.0:1.0:0.0:0.0	.	128	Q86UV6-2	.	I	128	ENSP00000378665:V128I;ENSP00000285805:V128I	ENSP00000285805:V128I	V	-	1	0	TRIM74	72074243	0.146000	0.22672	0.997000	0.53966	0.212000	0.24457	1.560000	0.36331	1.412000	0.46977	0.184000	0.17185	GTC	TRIM74	-	NULL	ENSG00000155428		0.672	TRIM74-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TRIM74	HGNC	protein_coding	OTTHUMT00000252093.1	11	0.00	0	C	NM_198853		72436307	72436307	-1	no_errors	ENST00000285805	ensembl	human	known	69_37n	missense	9	30.77	4	SNP	1.000	T
TRIP12	9320	genome.wustl.edu	37	2	230643194	230643194	+	Silent	SNP	G	G	A			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr2:230643194G>A	ENST00000283943.5	-	35	5272	c.5094C>T	c.(5092-5094)cgC>cgT	p.R1698R	TRIP12_ENST00000389044.4_Silent_p.R1746R|TRIP12_ENST00000389045.3_Silent_p.R1428R	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1698					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTCCTAAGAAGCGAAACTTCA	0.423																																						dbGAP											0													163.0	161.0	162.0					2																	230643194		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.5094C>T	2.37:g.230643194G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	pfam_HECT,superfamily_HECT,superfamily_ARM-type_fold,smart_HECT,pfscan_HECT,pfscan_WWE-dom	p.R1698	ENST00000283943.5	37	c.5094	CCDS33391.1	2																																																																																			TRIP12	-	pfam_HECT,superfamily_HECT,smart_HECT,pfscan_HECT	ENSG00000153827		0.423	TRIP12-001	KNOWN	basic|CCDS	protein_coding	TRIP12	HGNC	protein_coding	OTTHUMT00000331861.3	220	0.00	0	G	NM_004238		230643194	230643194	-1	no_errors	ENST00000283943	ensembl	human	known	69_37n	silent	176	14.56	30	SNP	0.997	A
UGGT2	55757	genome.wustl.edu	37	13	96555315	96555315	+	Splice_Site	SNP	C	C	T			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chr13:96555315C>T	ENST00000376747.3	-	21	2366		c.e21-1			NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2						cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						CACTTGTTTTCTGCAAACATA	0.318																																						dbGAP											0													39.0	41.0	40.0					13																	96555315		2202	4295	6497	-	-	-	SO:0001630	splice_region_variant	0			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.2296-1G>A	13.37:g.96555315C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Splice_Site	SNP	-	e21-1	ENST00000376747.3	37	c.2296-1	CCDS9480.1	13	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780603	0.49891	.	.	ENSG00000102595	ENST00000376747	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.005	0.58699	0.0:0.9262:0.0:0.0738	.	.	.	.	.	-1	.	.	.	-	.	.	UGGT2	95353316	1.000000	0.71417	1.000000	0.80357	0.526000	0.34562	4.701000	0.61810	2.669000	0.90835	0.650000	0.86243	.	UGGT2	-	-	ENSG00000102595		0.318	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UGGT2	HGNC	protein_coding	OTTHUMT00000045507.1	87	0.00	0	C	NM_020121	Intron	96555315	96555315	-1	no_errors	ENST00000376747	ensembl	human	known	69_37n	splice_site	57	24.68	19	SNP	1.000	T
ZCCHC12	170261	genome.wustl.edu	37	X	117959237	117959237	+	Missense_Mutation	SNP	C	C	G			TCGA-E2-A1B1-01A-21D-A12Q-09	TCGA-E2-A1B1-10A-01D-A12Q-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	a6e77a14-e5e5-452e-a46f-5629ee8228e3	6aec902b-6a2e-4cfa-b294-785057c147ef	g.chrX:117959237C>G	ENST00000310164.2	+	4	537	c.30C>G	c.(28-30)aaC>aaG	p.N10K		NM_173798.2	NP_776159.1	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	10					BMP signaling pathway (GO:0030509)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	22						GTGTCGGTAACAGCCGGCGGC	0.522																																						dbGAP											0													68.0	62.0	64.0					X																	117959237		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK122676	CCDS14574.1	Xq24	2013-10-11			ENSG00000174460	ENSG00000174460		"""Zinc fingers, CCHC domain containing"", ""Paraneoplastic Ma antigens"""	27273	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 7A"""	300701				21739307, 19578717	Standard	NM_173798		Approved	FLJ16123, SIZN, SIZN1, PNMA7A	uc004equ.3	Q6PEW1	OTTHUMG00000022261	ENST00000310164.2:c.30C>G	X.37:g.117959237C>G	ENSP00000308921:p.Asn10Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KV48|Q6PID5|Q8N1C1	Missense_Mutation	SNP	superfamily_Znf_CCHC	p.N10K	ENST00000310164.2	37	c.30	CCDS14574.1	X	.	.	.	.	.	.	.	.	.	.	C	5.278	0.236686	0.10023	.	.	ENSG00000174460	ENST00000310164	T	0.32515	1.45	3.05	-0.508	0.11980	.	0.646140	0.12825	N	0.436108	T	0.20618	0.0496	L	0.44542	1.39	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.24764	-1.0151	10	0.59425	D	0.04	-1.5372	2.4443	0.04502	0.2256:0.4059:0.0:0.3684	.	10	Q6PEW1	ZCH12_HUMAN	K	10	ENSP00000308921:N10K	ENSP00000308921:N10K	N	+	3	2	ZCCHC12	117843265	0.650000	0.27331	0.084000	0.20598	0.726000	0.41606	-0.640000	0.05440	-0.243000	0.09653	-0.307000	0.09154	AAC	ZCCHC12	-	NULL	ENSG00000174460		0.522	ZCCHC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZCCHC12	HGNC	protein_coding	OTTHUMT00000058014.1	84	0.00	0	C	NM_173798		117959237	117959237	+1	no_errors	ENST00000310164	ensembl	human	known	69_37n	missense	56	15.15	10	SNP	0.081	G
