U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 54857, updated on 5-Mar-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
Xq13.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (70423314..70433381)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (68856634..68866693)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: 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

Go to the top of the pageHelp

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

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
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)

Go to the top of the page Help

NEW Try the new Transcript table

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_2023_10

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

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous