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GNPAT glyceronephosphate O-acyltransferase [ Homo sapiens (human) ]

Gene ID: 8443, updated on 2-Nov-2024

Summary

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Official Symbol
GNPATprovided by HGNC
Official Full Name
glyceronephosphate O-acyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:4416
See related
Ensembl:ENSG00000116906 MIM:602744; AllianceGenome:HGNC:4416
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DAPAT; RCDP2; DAP-AT; DHAPAT
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 isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
Expression
Ubiquitous expression in testis (RPKM 20.9), heart (RPKM 16.9) and 25 other tissues See more
Orthologs
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Genomic context

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See GNPAT in Genome Data Viewer
Location:
1q42.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (231241212..231277973)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (230624475..230661237)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (231376958..231413719)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene tripartite motif containing 67 Neighboring gene NANOG hESC enhancer GRCh37_chr1:231319561-231320089 Neighboring gene TRIM67 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:231350707-231351208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1949 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:231352923-231353422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:231356573-231357073 Neighboring gene 40S small subunit processome assembly factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:231376971-231377860 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:231420145-231420646 Neighboring gene RNA, 5S ribosomal pseudogene 80 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:231472900-231473775 Neighboring gene exocyst complex component 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Etherphospholipid biosynthesis and dihydroxyactetone-phosphate acyltransferase: resolution of the genomic organization of the human gnpat gene and its use in the identification of novel mutations. Ofman R, et al. Biochem Biophys Res Commun, 2001 Mar 2. PMID 11237722
  2. GNPAT rs11558492 is not a Major Modifier of Iron Status: Study of Italian Hemochromatosis Patients and Blood Donors. Greni F, et al. Ann Hepatol, 2017 May-Jun. PMID 28425416
  3. Topography of ether phospholipid biosynthesis. Hardeman D, et al. Biochim Biophys Acta, 1989 Nov 6. PMID 2804060
  4. Genetic adaptation of skin pigmentation in highland Tibetans. Yang Z, et al. Proc Natl Acad Sci U S A, 2022 Oct 4. PMID 36161951, Free PMC Article
  5. Reduction of Ether-Type Glycerophospholipids, Plasmalogens, by NF-κB Signal Leading to Microglial Activation. Hossain MS, et al. J Neurosci, 2017 Apr 12. PMID 28292831, Free PMC Article

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic adaptation of skin pigmentation in highland Tibetans.
    Title: Genetic adaptation of skin pigmentation in highland Tibetans.
  2. Increased frequency of GNPAT p.D519G in compound HFE p.C282Y/p.H63D heterozygotes with elevated serum ferritin levels.
    Title: Increased frequency of GNPAT p.D519G in compound HFE p.C282Y/p.H63D heterozygotes with elevated serum ferritin levels.
  3. Stabilization of FASN by ACAT1-mediated GNPAT acetylation promotes lipid metabolism and hepatocarcinogenesis.
    Title: Stabilization of FASN by ACAT1-mediated GNPAT acetylation promotes lipid metabolism and hepatocarcinogenesis.
  4. GNPAT and USP30-mediated stabilization of DRP1 play a critical role in the development of hepatocellular carcinoma
    Title: Amplification of Glyceronephosphate O-Acyltransferase and Recruitment of USP30 Stabilize DRP1 to Promote Hepatocarcinogenesis.
  5. GNPAT p.D519G is strongly associated with markedly increased iron stores in p.C282Y homozygotes after correction for age, iron-related variables, and alcohol consumption.
    Title: GNPAT p.D519G is independently associated with markedly increased iron stores in HFE p.C282Y homozygotes.
  6. GNPAT rs11558492 is not a major modifier of iron status and is not associated with liver fibrosis in HFE-related Hemochromatosis patients.
    Title: GNPAT rs11558492 is not a Major Modifier of Iron Status: Study of Italian Hemochromatosis Patients and Blood Donors.
  7. Here, we report the characterization of the recombinant human DHAP acyl-transferase, which performs the first step in alkyl-DHAP synthesis.
    Title: Recombinant human dihydroxyacetonephosphate acyl-transferase characterization as an integral monotopic membrane protein.
  8. Reduction of GNPAT activated NF-kappaB in glial cell lines and microglia in cortex.
    Title: Reduction of Ether-Type Glycerophospholipids, Plasmalogens, by NF-κB Signal Leading to Microglial Activation.
  9. C282Y homozygotes referred for HFE testing commonly have a GNPAT variant. This GNPAT variant does not appear be a co-modifying gene affecting expression of HFE related hemochromatosis in this population. The GNPAT variant does not predict the severity of iron overload.
    Title:  GNPAT variant (D519G) is not associated with an elevated serum ferritin or iron removed by phlebotomy in patients referred for C282Y-linked hemochromatosis.
  10. The variant of the GNPAT gene showed the most significant association with severe iron overload.
    Title: Exome sequencing in HFE C282Y homozygous men with extreme phenotypes identifies a GNPAT variant associated with severe iron overload.
Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Rhizomelic chondrodysplasia punctata type 2
MedGen: C1857242 OMIM: 222765 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables glycerone-phosphate O-acyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycerone-phosphate O-acyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycerone-phosphate O-acyltransferase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in cerebellum morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in ether lipid biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ether lipid biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ether lipid biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in membrane organization IEA
Inferred from Electronic Annotation
more info
  
involved_in paranodal junction assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in phosphatidic acid biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in response to fatty acid IEA
Inferred from Electronic Annotation
more info
  
involved_in response to nutrient IEA
Inferred from Electronic Annotation
more info
  
involved_in response to starvation IEA
Inferred from Electronic Annotation
more info
  
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in synapse assembly IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 
located_in peroxisomal matrix TAS
Traceable Author Statement
more info
  
located_in peroxisomal membrane HDA PubMed 
is_active_in peroxisomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in peroxisomal membrane TAS
Traceable Author Statement
more info
  
located_in peroxisome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in peroxisome NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
dihydroxyacetone phosphate acyltransferase
Names
DHAP-AT
acyl-CoA:dihydroxyacetonephosphateacyltransferase
glycerone-phosphate O-acyltransferase
NP_001303279.1
NP_055051.1
XP_005273370.1
XP_054195169.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008240.2 RefSeqGene

    Range
    5040..41801
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001316350.2 → NP_001303279.1  dihydroxyacetone phosphate acyltransferase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AK297982, AL137801, BE222957, DC366380
    UniProtKB/TrEMBL
    Q53FI2, Q53H08
    Conserved Domains (1) summary
    cd07993
    Location:73 → 278
    LPLAT_DHAPAT-like; Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like

  2. NM_014236.4 → NP_055051.1  dihydroxyacetone phosphate acyltransferase isoform 1

    See identical proteins and their annotated locations for NP_055051.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ002190, AL137801, BE222957
    Consensus CDS
    CCDS1592.1
    UniProtKB/Swiss-Prot
    B4DNM9, O15228, Q5TBH7, Q9BWC2
    UniProtKB/TrEMBL
    Q53FI2, Q53H08
    Related
    ENSP00000355607.4, ENST00000366647.9
    Conserved Domains (2) summary
    cd07993
    Location:134 → 339
    LPLAT_DHAPAT-like; Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like
    PTZ00374
    Location:62 → 608
    PTZ00374; dihydroxyacetone phosphate acyltransferase; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    231241212..231277973
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005273313.5 → XP_005273370.1  dihydroxyacetone phosphate acyltransferase isoform X1

    UniProtKB/TrEMBL
    Q53FI2, Q53H08
    Conserved Domains (2) summary
    cd07993
    Location:133 → 338
    LPLAT_DHAPAT-like; Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like
    PTZ00374
    Location:61 → 607
    PTZ00374; dihydroxyacetone phosphate acyltransferase; Provisional

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    230624475..230661237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339194.1 → XP_054195169.1  dihydroxyacetone phosphate acyltransferase isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15228.1 GenPept UniProtKB/Swiss-Prot:O15228

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