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

Gene ID: 284161, updated on 5-Mar-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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Location:
17q22
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (59220511..59275970)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (60088603..60144069)
105.20220307 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

Bibliography

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Related articles in PubMed

  1. 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
  2. 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
  3. 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
  4. 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
  5. Mammalian glycerophosphodiester phosphodiesterases. Yanaka N. Biosci Biotechnol Biochem, 2007 Aug. PMID 17690467

See all (20) 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_2023_10

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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