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    GDPD1 glycerophosphodiester phosphodiesterase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 284161, updated on 28-Oct-2024

    Summary

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    Official Symbol
    GDPD1provided by HGNC
    Official Full Name
    glycerophosphodiester phosphodiesterase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:20883
    See related
    Ensembl:ENSG00000153982 MIM:616317; AllianceGenome:HGNC:20883
    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
    GDE4
    Summary
    This gene encodes a member of the glycerophosphodiester phosphodiesterase family of enzymes that catalyze the hydrolysis of deacylated glycerophospholipids to glycerol phosphate and alcohol. The encoded protein is localized to the cytoplasm and concentrates near the perinuclear region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
    Expression
    Broad expression in brain (RPKM 4.9), testis (RPKM 3.0) and 22 other tissues See more
    Orthologs
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    Genomic context

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    See GDPD1 in Genome Data Viewer
    Location:
    17q22
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (59220511..59275970)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (60088603..60144069)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (57297872..57353331)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene proline rich 11 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57259739-57260240 Neighboring gene speedy/RINGO cell cycle regulator family member E22, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57297898-57298448 Neighboring gene SMG8 nonsense mediated mRNA decay factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12505 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:57367429-57368276 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 17 Neighboring gene Sharpr-MPRA regulatory region 3101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:57409512-57410073 Neighboring gene yippee like 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:57443013-57443782 Neighboring gene microRNA 4729

    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. A novel splice variant of human gene GDPD1 is mainly expressed in human ovary and small intestine. Wu M, et al. Int J Mol Med, 2003 Dec. PMID 14612981
    2. Isolation, characterization and molecular 3D model of human GDE4, a novel membrane protein containing glycerophosphodiester phosphodiesterase domain. Chang PA, et al. Mol Membr Biol, 2008 Sep. PMID 18991142
    3. Mammalian glycerophosphodiester phosphodiesterases. Yanaka N. Biosci Biotechnol Biochem, 2007 Aug. PMID 17690467
    4. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7. Kitakaze K, et al. J Lipid Res, 2021. PMID 34673020, Free PMC Article
    5. Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa. de Bruijn SE, et al. Am J Hum Genet, 2020 Nov 5. PMID 33022222, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7.
      Title: Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7.
    2. Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa.
      Title: Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa.
    3. 3-D model provides the structural information; subcellular localization is in the cytoplasm; over-expression of GDE4 did not induce neurite formation or change cell morphology
      Title: Isolation, characterization and molecular 3D model of human GDE4, a novel membrane protein containing glycerophosphodiester phosphodiesterase domain.
    4. A novel splice variant of the gene is mainly expressed in human ovary and small intestine.
      Title: A novel splice variant of human gene GDPD1 is mainly expressed in human ovary and small intestine.
    Submit: New GeneRIF Correction

    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

    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

    Clone Names

    • FLJ27503, FLJ37451, MGC35046

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables lysophospholipase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lysophospholipase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoric diester hydrolase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphoric diester hydrolase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in N-acylethanolamine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within N-acylethanolamine metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in N-acylethanolamine metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycerophospholipid catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane HDA PubMed 
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    lysophospholipase D GDPD1
    Names
    glycerophosphodiester phosphodiesterase 4
    glycerophosphodiester phosphodiesterase domain-containing protein 1
    NP_001159465.1
    NP_001159466.1
    NP_872375.2
    XP_016880010.1
    XP_054171806.1

    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.

    mRNA and Protein(s)

    1. NM_001165993.2 → NP_001159465.1  lysophospholipase D GDPD1 isoform 3

      See identical proteins and their annotated locations for NP_001159465.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and 3' coding region, compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC099850, AI478202, AY271346
      Consensus CDS
      CCDS58583.1
      UniProtKB/Swiss-Prot
      Q8N9F7
      Related
      ENSP00000463273.1, ENST00000581140.5
      Conserved Domains (1) summary
      cd08612
      Location:14 → 269
      GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins

    2. NM_001165994.2 → NP_001159466.1  lysophospholipase D GDPD1 isoform 2

      See identical proteins and their annotated locations for NP_001159466.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and 3' coding region, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC099850, BC034432
      Consensus CDS
      CCDS58584.1
      UniProtKB/Swiss-Prot
      Q8N9F7
      Related
      ENSP00000464690.1, ENST00000581276.5
      Conserved Domains (1) summary
      cd08612
      Location:14 → 279
      GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins

    3. NM_182569.4 → NP_872375.2  lysophospholipase D GDPD1 isoform 1

      See identical proteins and their annotated locations for NP_872375.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC091059, AC099850, AI478202, AK094770
      Consensus CDS
      CCDS11616.1
      UniProtKB/Swiss-Prot
      A8W735, Q56VR1, Q8N4E3, Q8N9F7
      Related
      ENSP00000284116.4, ENST00000284116.9
      Conserved Domains (1) summary
      cd08612
      Location:14 → 311
      GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      59220511..59275970
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017024521.2 → XP_016880010.1  lysophospholipase D GDPD1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      60088603..60144069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315831.1 → XP_054171806.1  lysophospholipase D GDPD1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N9F7.2 GenPept UniProtKB/Swiss-Prot:Q8N9F7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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