Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	8443
Gene name	Glyceronephosphate O-acyltransferase
Gene symbol	GNPAT
Synonyms (NCBI Gene)	DAP-ATDAPATDHAPATRCDP2
Chromosome	1
Chromosome location	1q42.2
Summary	This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoform

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121434439	G>A	Pathogenic	Missense variant, coding sequence variant
rs121434440	C>T	Pathogenic	Missense variant, coding sequence variant
rs777894746	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1442079596	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1558334598	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1558334625	->TT	Pathogenic	Frameshift variant, coding sequence variant
rs1571946866	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1571950208	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1571957148	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1571960363	G>A	Pathogenic	Intron variant

115

Show/Hide all (115)

miRTarBase ID	miRNA	Experiments	Reference
MIRT030370	hsa-miR-24-3p	Microarray	19748357
MIRT043262	hsa-miR-331-3p	CLASH	23622248
MIRT1025045	hsa-miR-1208	CLIP-seq
MIRT1025046	hsa-miR-1236	CLIP-seq
MIRT1025047	hsa-miR-1266	CLIP-seq
MIRT1025048	hsa-miR-2054	CLIP-seq
MIRT1025049	hsa-miR-2117	CLIP-seq
MIRT1025050	hsa-miR-339-5p	CLIP-seq
MIRT1025051	hsa-miR-3613-5p	CLIP-seq
MIRT1025052	hsa-miR-3664-3p	CLIP-seq
MIRT1025053	hsa-miR-3682-5p	CLIP-seq
MIRT1025054	hsa-miR-4273	CLIP-seq
MIRT1025055	hsa-miR-4330	CLIP-seq
MIRT1025056	hsa-miR-4518	CLIP-seq
MIRT1025057	hsa-miR-4711-3p	CLIP-seq
MIRT1025058	hsa-miR-4760-3p	CLIP-seq
MIRT1025059	hsa-miR-4764-5p	CLIP-seq
MIRT1025060	hsa-miR-4789-3p	CLIP-seq
MIRT1025061	hsa-miR-4803	CLIP-seq
MIRT1025062	hsa-miR-505	CLIP-seq
MIRT1025063	hsa-miR-548n	CLIP-seq
MIRT1025064	hsa-miR-548t	CLIP-seq
MIRT1025065	hsa-miR-561	CLIP-seq
MIRT1025066	hsa-miR-593	CLIP-seq
MIRT1025067	hsa-miR-670	CLIP-seq
MIRT1025068	hsa-miR-759	CLIP-seq
MIRT1025045	hsa-miR-1208	CLIP-seq
MIRT1025046	hsa-miR-1236	CLIP-seq
MIRT2003974	hsa-miR-1265	CLIP-seq
MIRT1025047	hsa-miR-1266	CLIP-seq
MIRT1025048	hsa-miR-2054	CLIP-seq
MIRT1025049	hsa-miR-2117	CLIP-seq
MIRT1025050	hsa-miR-339-5p	CLIP-seq
MIRT2003975	hsa-miR-3605-5p	CLIP-seq
MIRT1025051	hsa-miR-3613-5p	CLIP-seq
MIRT1025052	hsa-miR-3664-3p	CLIP-seq
MIRT1025053	hsa-miR-3682-5p	CLIP-seq
MIRT2003976	hsa-miR-4270	CLIP-seq
MIRT1025054	hsa-miR-4273	CLIP-seq
MIRT1025055	hsa-miR-4330	CLIP-seq
MIRT2003977	hsa-miR-4441	CLIP-seq
MIRT1025056	hsa-miR-4518	CLIP-seq
MIRT2003978	hsa-miR-4693-3p	CLIP-seq
MIRT1025057	hsa-miR-4711-3p	CLIP-seq
MIRT2003979	hsa-miR-4712-3p	CLIP-seq
MIRT1025059	hsa-miR-4764-5p	CLIP-seq
MIRT1025066	hsa-miR-593	CLIP-seq
MIRT1025067	hsa-miR-670	CLIP-seq
MIRT1025068	hsa-miR-759	CLIP-seq
MIRT2003974	hsa-miR-1265	CLIP-seq
MIRT1025047	hsa-miR-1266	CLIP-seq
MIRT1025050	hsa-miR-339-5p	CLIP-seq
MIRT2003975	hsa-miR-3605-5p	CLIP-seq
MIRT1025052	hsa-miR-3664-3p	CLIP-seq
MIRT2003976	hsa-miR-4270	CLIP-seq
MIRT2003977	hsa-miR-4441	CLIP-seq
MIRT1025056	hsa-miR-4518	CLIP-seq
MIRT2003979	hsa-miR-4712-3p	CLIP-seq
MIRT1025067	hsa-miR-670	CLIP-seq
MIRT1025046	hsa-miR-1236	CLIP-seq
MIRT2465379	hsa-miR-642a	CLIP-seq
MIRT1025045	hsa-miR-1208	CLIP-seq
MIRT1025046	hsa-miR-1236	CLIP-seq
MIRT1025047	hsa-miR-1266	CLIP-seq
MIRT2540632	hsa-miR-2110	CLIP-seq
MIRT2540633	hsa-miR-2115	CLIP-seq
MIRT1025049	hsa-miR-2117	CLIP-seq
MIRT1025052	hsa-miR-3664-3p	CLIP-seq
MIRT2540634	hsa-miR-3977	CLIP-seq
MIRT2003976	hsa-miR-4270	CLIP-seq
MIRT2540635	hsa-miR-4271	CLIP-seq
MIRT1025054	hsa-miR-4273	CLIP-seq
MIRT2540636	hsa-miR-4318	CLIP-seq
MIRT1025055	hsa-miR-4330	CLIP-seq
MIRT2003977	hsa-miR-4441	CLIP-seq
MIRT1025056	hsa-miR-4518	CLIP-seq
MIRT2540637	hsa-miR-4520a-5p	CLIP-seq
MIRT2540638	hsa-miR-4520b-5p	CLIP-seq
MIRT2003979	hsa-miR-4712-3p	CLIP-seq
MIRT2540639	hsa-miR-4725-3p	CLIP-seq
MIRT2540640	hsa-miR-491-5p	CLIP-seq
MIRT2540641	hsa-miR-516a-3p	CLIP-seq
MIRT2540642	hsa-miR-541	CLIP-seq
MIRT2540643	hsa-miR-548g	CLIP-seq
MIRT2540644	hsa-miR-614	CLIP-seq
MIRT2465379	hsa-miR-642a	CLIP-seq
MIRT2540645	hsa-miR-654-5p	CLIP-seq
MIRT1025068	hsa-miR-759	CLIP-seq
MIRT1025045	hsa-miR-1208	CLIP-seq
MIRT1025046	hsa-miR-1236	CLIP-seq
MIRT1025047	hsa-miR-1266	CLIP-seq
MIRT2540632	hsa-miR-2110	CLIP-seq
MIRT2540633	hsa-miR-2115	CLIP-seq
MIRT1025049	hsa-miR-2117	CLIP-seq
MIRT1025052	hsa-miR-3664-3p	CLIP-seq
MIRT2540634	hsa-miR-3977	CLIP-seq
MIRT2003976	hsa-miR-4270	CLIP-seq
MIRT2540635	hsa-miR-4271	CLIP-seq
MIRT1025054	hsa-miR-4273	CLIP-seq
MIRT2540636	hsa-miR-4318	CLIP-seq
MIRT1025055	hsa-miR-4330	CLIP-seq
MIRT2003977	hsa-miR-4441	CLIP-seq
MIRT1025056	hsa-miR-4518	CLIP-seq
MIRT2540637	hsa-miR-4520a-5p	CLIP-seq
MIRT2540638	hsa-miR-4520b-5p	CLIP-seq
MIRT2003979	hsa-miR-4712-3p	CLIP-seq
MIRT2540639	hsa-miR-4725-3p	CLIP-seq
MIRT2540640	hsa-miR-491-5p	CLIP-seq
MIRT2540641	hsa-miR-516a-3p	CLIP-seq
MIRT2540642	hsa-miR-541	CLIP-seq
MIRT2540643	hsa-miR-548g	CLIP-seq
MIRT2540644	hsa-miR-614	CLIP-seq
MIRT2465379	hsa-miR-642a	CLIP-seq
MIRT2540645	hsa-miR-654-5p	CLIP-seq
MIRT1025068	hsa-miR-759	CLIP-seq

Show/Hide all (33)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0005777	Component	Peroxisome	IDA	15687349
GO:0005777	Component	Peroxisome	IEA
GO:0005777	Component	Peroxisome	NAS	9459311
GO:0005778	Component	Peroxisomal membrane	HDA	21525035
GO:0005778	Component	Peroxisomal membrane	IBA
GO:0005778	Component	Peroxisomal membrane	IEA
GO:0005778	Component	Peroxisomal membrane	TAS
GO:0005782	Component	Peroxisomal matrix	TAS
GO:0005829	Component	Cytosol	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006650	Process	Glycerophospholipid metabolic process	IEA
GO:0006654	Process	Phosphatidic acid biosynthetic process	TAS
GO:0007416	Process	Synapse assembly	IEA
GO:0008374	Function	O-acyltransferase activity	IEA
GO:0008611	Process	Ether lipid biosynthetic process	IBA
GO:0008611	Process	Ether lipid biosynthetic process	IDA	15687349
GO:0008611	Process	Ether lipid biosynthetic process	IEA
GO:0008611	Process	Ether lipid biosynthetic process	IEA
GO:0008611	Process	Ether lipid biosynthetic process	TAS
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0016287	Function	Glycerone-phosphate O-acyltransferase activity	IBA
GO:0016287	Function	Glycerone-phosphate O-acyltransferase activity	IDA	8186247, 9536089, 10395968, 11152660, 15687349
GO:0016287	Function	Glycerone-phosphate O-acyltransferase activity	IEA
GO:0016287	Function	Glycerone-phosphate O-acyltransferase activity	TAS
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0021587	Process	Cerebellum morphogenesis	IEA
GO:0030054	Component	Cell junction	IDA
GO:0030913	Process	Paranodal junction assembly	IEA
GO:0042552	Process	Myelination	IEA
GO:0061024	Process	Membrane organization	IEA

MIM	HGNC	e!Ensembl
602744	4416	ENSG00000116906

O15228

Protein name

Dihydroxyacetone phosphate acyltransferase (DAP-AT) (DAPAT) (DHAP-AT) (EC 2.3.1.42) (Acyl-CoA:dihydroxyacetonephosphateacyltransferase) (Glycerone-phosphate O-acyltransferase)

Protein function

Dihydroxyacetonephosphate acyltransferase catalyzing the first step in the biosynthesis of plasmalogens, a subset of phospholipids that differ from other glycerolipids by having an alkyl chain attached through a vinyl ether linkage at the sn-1 p

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01553	Acyltransferase	138 → 283	Acyltransferase	Family

Sequence

MESSSSSNSYFSVGPTSPSAVVLLYSKELKKWDEFEDILEERRHVSDLKFAMKCYTPLVY
KGITPCKPIDIKCSVLNSEEIHYVIKQLSKESLQSVDVLREEVSEILDEMSHKLRLGAIR
FCAFTLSKVFKQIFSKVCVNEEGIQKLQRAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDL
PVPVIAAGMDFLGMKMVGELLRMSGAFFMRRTFGGNKLYWAVFSEYVKTMLRNGYAPVEF
FLEGTRSRSAKTLTPKFGLLNIVMEPFFKREVFDTYLVPISISYDKILEETLYVYELLGV
PKPKESTTGLLKARKILSENFGSIHVYFGDPVSLRSLAAGRMSRSSYNLVPRYIPQKQSE
DMHAFVTEVAYKMELLQIENMVLSPWTLIVAVLLQNRPSMDFDALVEKTLWLKGLTQAFG
GFLIWPDNKPAEEVVPASILLHSNIASLVKDQVILKVDSGDSEVVDGLMLQHITLLMCSA
YRNQLLNIFVRPSLVAVALQMTPGFRKEDVYSCFRFLRDVFADEFIFLPGNTLKDFEEGC
YLLCKSEAIQVTTKDILVTEKGNTVLEFLVGLFKPFVESYQIICKYLLSEEEDHFSEEQY
LAAVRKFTSQLLDQGTSQCYDVLSSDVQKNALAACVRLGVVEKKKINNNCIFNVNEPATT
KLEEMLGCKTPIGKPATAKL

Sequence length

680

Interactions

View interactions

	KEGG		Reactome
	Glycerophospholipid metabolism Peroxisome		Synthesis of PA Plasmalogen biosynthesis Peroxisomal protein import

158

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
GNPAT-related disorder	Likely pathogenic	rs777894746	RCV003411694
Rhizomelic chondrodysplasia punctata	Pathogenic; Likely pathogenic	rs2102825068, rs121434440	RCV001526991 RCV003234895
Rhizomelic chondrodysplasia punctata type 2	Pathogenic; Likely pathogenic	rs745869264, rs1685194348, rs749069446, rs1283169932, rs121434439, rs121434440, rs1558334625, rs1571950208, rs1571957148, rs2527028635, rs1185964193, rs2527044284, rs2527024495, rs2526967162, rs2527024941 View all (22 more)	RCV001844353 RCV001782213 RCV004571718 RCV004571191 RCV000007243 RCV000007244 RCV000007245 RCV000007246 RCV000007247 RCV003468285 RCV003461709 RCV003461710 RCV003468286 RCV003468287 RCV003468288 RCV003468289 RCV003461711 RCV003468290 RCV003468291 RCV003468292 RCV003468293 RCV003468294 RCV003468295 RCV003461712 RCV003468296 RCV003468297 RCV003461713 RCV004576695 RCV004576696 RCV004576697 RCV004576698 RCV004576699 RCV004576700 RCV000029141 RCV000029142 RCV000029143 RCV000825526

Show/Hide Unknown Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Likely benign; Benign	rs116024301, rs41305723	RCV005917567 RCV005900021
Cervical cancer	Likely benign; Conflicting classifications of pathogenicity	rs116024301, rs34613633	RCV005917569 RCV005892297
Clear cell carcinoma of kidney	Benign	rs6659098	RCV005892924
Colon adenocarcinoma	Conflicting classifications of pathogenicity	rs34613633, rs142283145	RCV005892295 RCV005898853
Colorectal cancer	Conflicting classifications of pathogenicity	rs34613633	RCV005892298
Familial cancer of breast	Conflicting classifications of pathogenicity	rs34613633	RCV005892294
Hepatocellular carcinoma	Benign	rs6659098	RCV005892923
Lung cancer	Likely benign; Benign	rs116024301, rs6659098, rs41305723	RCV005917570 RCV005892925 RCV005900023
Malignant tumor of esophagus	Likely benign; Conflicting classifications of pathogenicity	rs116024301, rs34613633	RCV005917568 RCV005892296
Ovarian serous cystadenocarcinoma	Likely benign; Benign	rs6675174, rs41305723	RCV005917899 RCV005900022
Prostate cancer	Uncertain significance	rs193920851	RCV000149206
Sarcoma	Likely benign	rs774251102	RCV005935036
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs34613633	RCV005892299
Uterine corpus endometrial carcinoma	Benign	rs6659098	RCV005892926

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Chondrodysplasia Punctata Rhizomelic	Inhibit	10553003
Chondrodysplasia Punctata Rhizomelic	Associate	25439727, 34110102, 8466247
Fibrosis	Associate	30145563
Hemochromatosis	Associate	27740525, 28425416, 32652459
Inflammation	Associate	23020131
Iron Overload	Associate	25605615, 27740525, 32652459
Melanoma	Associate	23020131
Zellweger Syndrome	Associate	3706414

GNPAT (glyceronephosphate O-acyltransferase)