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    GDPD2 glycerophosphodiester phosphodiesterase domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 54857, updated on 10-Dec-2024

    Summary

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    Official Symbol
    GDPD2provided by HGNC
    Official Full Name
    glycerophosphodiester phosphodiesterase domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:25974
    See related
    Ensembl:ENSG00000130055 MIM:300940; AllianceGenome:HGNC:25974
    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
    GDE3; OBDPF
    Summary
    This gene encodes a member of the glycerophosphodiester phosphodiesterase enzyme family. The encoded protein hydrolyzes glycerophosphoinositol to produce inositol 1-phosphate and glycerol. This protein may have a role in osteoblast differentiation and growth. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2010]
    Expression
    Biased expression in spleen (RPKM 25.5), skin (RPKM 21.4) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GDPD2 in Genome Data Viewer
    Location:
    Xq13.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (70423314..70433381)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (68856634..68866693)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (69643164..69653231)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene kinesin family member 4A Neighboring gene TRAPPC2L pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:69622427-69622649 Neighboring gene RNY4 pseudogene 23 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:69642130-69643118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:69643119-69644107 Neighboring gene uncharacterized LOC105373244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:69655249-69655749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:69664203-69664989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20891 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:69674628-69675054 Neighboring gene RNA, U4 small nuclear 81, pseudogene Neighboring gene DLG3 antisense RNA 1 Neighboring gene discs large MAGUK scaffold protein 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Glycerophosphodiesterase 3 (GDE3) is a lysophosphatidylinositol-specific ectophospholipase C acting as an endocannabinoid signaling switch. Briand-Mésange F, et al. J Biol Chem, 2020 Nov 13. PMID 32917725, Free PMC Article
    2. The developmentally regulated osteoblast phosphodiesterase GDE3 is glycerophosphoinositol-specific and modulates cell growth. Corda D, et al. J Biol Chem, 2009 Sep 11. PMID 19596859, Free PMC Article
    3. Novel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation. Yanaka N, et al. J Biol Chem, 2003 Oct 31. PMID 12933806
    4. Negative regulation of urokinase receptor activity by a GPI-specific phospholipase C in breast cancer cells. van Veen M, et al. Elife, 2017 Aug 29. PMID 28849762, Free PMC Article
    5. The DNA sequence of the human X chromosome. Ross MT, et al. Nature, 2005 Mar 17. PMID 15772651, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Glycerophosphodiesterase 3 (GDE3) is a lysophosphatidylinositol-specific ectophospholipase C acting as an endocannabinoid signaling switch.
      Title: Glycerophosphodiesterase 3 (GDE3) is a lysophosphatidylinositol-specific ectophospholipase C acting as an endocannabinoid signaling switch.
    2. The results establish GDE3 as a negative regulator of the uPAR signaling network and, furthermore, highlight GPI-anchor hydrolysis as a cell-intrinsic mechanism to alter cell behavior.
      Title: Negative regulation of urokinase receptor activity by a GPI-specific phospholipase C in breast cancer cells.
    3. GDE3 substrate GroPIns is a candidate mediator for osteoblast proliferation
      Title: The developmentally regulated osteoblast phosphodiesterase GDE3 is glycerophosphoinositol-specific and modulates cell growth.
    4. GDE3 is a novel seven-transmembrane protein with a GP-PDE-like extracellular motif expressed during osteoblast differentiation that accelerates the program of osteoblast differentiation and is involved in morphological change of cells
      Title: Novel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20207

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glycerophosphodiester phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables glycerophosphoinositol inositolphosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin filament organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in actin filament IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lamellipodium IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    glycerophosphoinositol inositolphosphodiesterase GDPD2
    Names
    glycerophosphodiester phosphodiesterase 3
    glycerophosphodiester phosphodiesterase domain-containing protein 2
    osteoblast differentiation promoting factor
    NP_001164662.1
    NP_001164663.1
    NP_001164664.1
    NP_060181.2
    XP_011529279.1
    XP_054183267.1

    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_016413.1 RefSeqGene

      Range
      5284..15351
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171191.2 → NP_001164662.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 3

      See identical proteins and their annotated locations for NP_001164662.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG. Variants 3 and 4 encode the same isoform (3), which is shorter than isoform 1.
      Source sequence(s)
      AI277430, AK299255
      Consensus CDS
      CCDS55438.1
      UniProtKB/Swiss-Prot
      Q9HCC8
      Related
      ENSP00000444601.1, ENST00000538649.5
      Conserved Domains (1) summary
      cd08609
      Location:123 → 433
      GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins

    2. NM_001171192.2 → NP_001164663.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 1

      See identical proteins and their annotated locations for NP_001164663.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AI277430, AK301025, AL139398
      Consensus CDS
      CCDS55437.1
      UniProtKB/Swiss-Prot
      Q9HCC8
      Related
      ENSP00000414019.2, ENST00000453994.6
      Conserved Domains (1) summary
      cl14615
      Location:202 → 563
      PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

    3. NM_001171193.2 → NP_001164664.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 3

      See identical proteins and their annotated locations for NP_001164664.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG. Variants 3 and 4 encode the same isoform (3), which is shorter than isoform 1.
      Source sequence(s)
      AI277430, AK316035, AL139398
      Consensus CDS
      CCDS55438.1
      UniProtKB/Swiss-Prot
      Q9HCC8
      Related
      ENSP00000445982.1, ENST00000536730.5
      Conserved Domains (1) summary
      cd08609
      Location:123 → 433
      GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins

    4. NM_017711.4 → NP_060181.2  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform 2

      See identical proteins and their annotated locations for NP_060181.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, which results in a frameshift, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      AB048363, AL139398
      Consensus CDS
      CCDS14402.1
      UniProtKB/Swiss-Prot
      B4DRH4, B4DVC9, Q9HCC8, Q9NXJ6
      Related
      ENSP00000363503.3, ENST00000374382.4
      Conserved Domains (1) summary
      cd08609
      Location:202 → 512
      GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      70423314..70433381
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011530977.2 → XP_011529279.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform X1

      Conserved Domains (2) summary
      cd08609
      Location:75 → 385
      GDPD_GDE3; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins
      pfam03009
      Location:102 → 344
      GDPD; Glycerophosphoryl diester phosphodiesterase family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      68856634..68866693
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327292.1 → XP_054183267.1  glycerophosphoinositol inositolphosphodiesterase GDPD2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCC8.1 GenPept UniProtKB/Swiss-Prot:Q9HCC8

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