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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
    mouse all
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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
    		Compare labs

    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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