Glycerophosphodiester phosphodiesterases (GDPDs; EC 3.1.4.46), such as GDPD5, are involved in glycerol metabolism (Lang et al., 2008 [PubMed 17578682]).[supplied by OMIM, Jan 2010] See more...

Aliases for GDPD5 Gene

Aliases for GDPD5 Gene

  • Glycerophosphodiester Phosphodiesterase Domain Containing 5 2 3 5
  • Glycerophosphodiester Phosphodiesterase Domain-Containing Protein 5 3 4
  • Glycerophosphodiester Phosphodiesterase 2 3 4
  • GDE2 3 4
  • EC 3.1.4.11 4
  • PP1665 3

External Ids for GDPD5 Gene

Previous GeneCards Identifiers for GDPD5 Gene

  • GC11M074824
  • GC11M075145
  • GC11M071442

Summaries for GDPD5 Gene

Entrez Gene Summary for GDPD5 Gene

  • Glycerophosphodiester phosphodiesterases (GDPDs; EC 3.1.4.46), such as GDPD5, are involved in glycerol metabolism (Lang et al., 2008 [PubMed 17578682]).[supplied by OMIM, Jan 2010]

GeneCards Summary for GDPD5 Gene

GDPD5 (Glycerophosphodiester Phosphodiesterase Domain Containing 5) is a Protein Coding gene. Among its related pathways are PI Metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include phosphoric diester hydrolase activity and glycerophosphodiester phosphodiesterase activity. An important paralog of this gene is GDPD2.

UniProtKB/Swiss-Prot Summary for GDPD5 Gene

  • Glycerophosphodiester phosphodiesterase that promotes neurite formation and drives spinal motor neuron differentiation (By similarity). Mediates the cleavage of glycosylphosphatidylinositol (GPI) anchor of target proteins: removes the GPI-anchor of RECK, leading to release RECK from the plasma membrane (By similarity). May contribute to the osmotic regulation of cellular glycerophosphocholine (By similarity).

Additional gene information for GDPD5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GDPD5 Gene

Genomics for GDPD5 Gene

GeneHancer (GH) Regulatory Elements for GDPD5 Gene

Promoters and enhancers for GDPD5 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GDPD5 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GDPD5

Top Transcription factor binding sites by QIAGEN in the GDPD5 gene promoter:
  • AML1a
  • AREB6
  • ARP-1
  • NF-1
  • POU2F1
  • POU2F1a
  • PPAR-alpha
  • RP58
  • ZIC2

Genomic Locations for GDPD5 Gene

Genomic Locations for GDPD5 Gene
chr11:75,434,640-75,525,941
(GRCh38/hg38)
Size:
91,302 bases
Orientation:
Minus strand
chr11:75,145,685-75,236,948
(GRCh37/hg19)
Size:
91,264 bases
Orientation:
Minus strand

Genomic View for GDPD5 Gene

Genes around GDPD5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDPD5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GDPD5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDPD5 Gene

Proteins for GDPD5 Gene

  • Protein details for GDPD5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WTR4-GDPD5_HUMAN
    Recommended name:
    Glycerophosphodiester phosphodiesterase domain-containing protein 5
    Protein Accession:
    Q8WTR4
    Secondary Accessions:
    • Q49AQ5
    • Q6UX76
    • Q7Z4S0
    • Q8N781
    • Q8NCB7
    • Q8TB77

    Protein attributes for GDPD5 Gene

    Size:
    605 amino acids
    Molecular mass:
    68586 Da
    Quaternary structure:
    • Interacts with PRDX1; forms a mixed-disulfide with PRDX1, leading to disrupt intramolecular disulfide bond between Cys-25 and Cys-571.
    SequenceCaution:
    • Sequence=AAP97686.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC11242.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GDPD5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GDPD5 Gene

Post-translational modifications for GDPD5 Gene

  • Intramolecular disulfide bond between Cys-25 and Cys-571 is reduced by PRDX1.
  • Glycosylation at Asn301, Asn336, Asn352, Asn374, and Asn448
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GDPD5 Gene

Domains & Families for GDPD5 Gene

Gene Families for GDPD5 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for GDPD5 Gene

Blocks:
  • Glycerophosphoryl diester phosphodiesterase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GDPD5 Gene

GenScript: Design optimal peptide antigens:
  • Glycerophosphodiester phosphodiesterase 2 (GDPD5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WTR4

UniProtKB/Swiss-Prot:

GDPD5_HUMAN :
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
Family:
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
genes like me logo Genes that share domains with GDPD5: view

Function for GDPD5 Gene

Molecular function for GDPD5 Gene

UniProtKB/Swiss-Prot Function:
Glycerophosphodiester phosphodiesterase that promotes neurite formation and drives spinal motor neuron differentiation (By similarity). Mediates the cleavage of glycosylphosphatidylinositol (GPI) anchor of target proteins: removes the GPI-anchor of RECK, leading to release RECK from the plasma membrane (By similarity). May contribute to the osmotic regulation of cellular glycerophosphocholine (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + H2O = 1D-myo-inositol 1,4,5-trisphosphate + a 1,2-diacyl-sn-glycerol + H(+); Xref=Rhea:RHEA:33179, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17815, ChEBI:CHEBI:58456, ChEBI:CHEBI:203600; EC=3.1.4.11; Evidence=. ;.

Enzyme Numbers (IUBMB) for GDPD5 Gene

Phenotypes From GWAS Catalog for GDPD5 Gene

Gene Ontology (GO) - Molecular Function for GDPD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004435 phosphatidylinositol phospholipase C activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0047389 glycerophosphocholine phosphodiesterase activity IEA --
genes like me logo Genes that share ontologies with GDPD5: view
genes like me logo Genes that share phenotypes with GDPD5: view

Animal Models for GDPD5 Gene

MGI Knock Outs for GDPD5:
  • Gdpd5 Gdpd5<tm1.1Itl>
  • Gdpd5 Gdpd5<tm1b(EUCOMM)Hmgu>

Animal Model Products

  • Taconic Biosciences Mouse Models for GDPD5

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GDPD5

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GDPD5 Gene

Localization for GDPD5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDPD5 Gene

Endomembrane system; Multi-pass membrane protein. Cytoplasm, perinuclear region. Cell projection, growth cone. Note=In a punctate perinuclear pattern. {ECO:0000250 UniProtKB:Q640M6}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GDPD5 gene
Compartment Confidence
plasma membrane 3
endoplasmic reticulum 3
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GDPD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030424 axon IEA --
genes like me logo Genes that share ontologies with GDPD5: view

Pathways & Interactions for GDPD5 Gene

genes like me logo Genes that share pathways with GDPD5: view

Gene Ontology (GO) - Biological Process for GDPD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0007399 nervous system development IEA --
GO:0021522 spinal cord motor neuron differentiation IEA --
GO:0021895 cerebral cortex neuron differentiation IEA --
GO:0031175 neuron projection development IEA --
genes like me logo Genes that share ontologies with GDPD5: view

No data available for SIGNOR curated interactions for GDPD5 Gene

Drugs & Compounds for GDPD5 Gene

No Compound Related Data Available

Transcripts for GDPD5 Gene

mRNA/cDNA for GDPD5 Gene

3 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
17 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GDPD5

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GDPD5 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: - - - - -
SP2: -
SP3: - - - - - - - - - - - -
SP4:
SP5: -
SP6: - - - - - - - -
SP7: -
SP8:
SP9:

ExUns: 22a · 22b ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28a · 28b
SP1: - -
SP2: - -
SP3: - -
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for GDPD5 Gene

GeneLoc Exon Structure for
GDPD5

Expression for GDPD5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GDPD5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GDPD5 Gene

This gene is overexpressed in Spleen (x8.1).

Protein differential expression in normal tissues from HIPED for GDPD5 Gene

This gene is overexpressed in Placenta (45.2) and Retina (23.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for GDPD5 Gene



Protein tissue co-expression partners for GDPD5 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GDPD5

SOURCE GeneReport for Unigene cluster for GDPD5 Gene:

Hs.503297

Evidence on tissue expression from TISSUES for GDPD5 Gene

  • Nervous system(4.4)
  • Eye(4.1)
  • Thyroid gland(4.1)
genes like me logo Genes that share expression patterns with GDPD5: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GDPD5 Gene

Orthologs for GDPD5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for GDPD5 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia GDPD5 31 30
  • 90.74 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GDPD5 31 30
  • 90.52 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gdpd5 17 31 30
  • 87.8 (n)
rat
(Rattus norvegicus)
Mammalia Gdpd5 30
  • 87.36 (n)
oppossum
(Monodelphis domestica)
Mammalia GDPD5 31
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GDPD5 31
  • 54 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDPD5 31 30
  • 70.47 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GDPD5 31
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gdpd5 30
  • 67.52 (n)
Str.8190 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.34080 30
zebrafish
(Danio rerio)
Actinopterygii LOC560645 30
  • 62.75 (n)
gdpd5b 31
  • 60 (a)
OneToMany
gdpd5a 31
  • 54 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 30 (a)
OneToMany
Species where no ortholog for GDPD5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for GDPD5 Gene

ENSEMBL:
Gene Tree for GDPD5 (if available)
TreeFam:
Gene Tree for GDPD5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GDPD5: view image

Paralogs for GDPD5 Gene

Paralogs for GDPD5 Gene

(3) SIMAP similar genes for GDPD5 Gene using alignment to 4 proteins:

  • GDPD5_HUMAN
  • E9PJU5_HUMAN
  • H0YEF5_HUMAN
  • Q9HBR3_HUMAN
genes like me logo Genes that share paralogs with GDPD5: view

Variants for GDPD5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GDPD5 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
736929 Benign: not provided 75,462,842(-) C/T SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
rs571353 - p.Ala480Thr

Additional dbSNP identifiers (rs#s) for GDPD5 Gene

Structural Variations from Database of Genomic Variants (DGV) for GDPD5 Gene

Variant ID Type Subtype PubMed ID
esv2671729 CNV deletion 23128226
esv2759838 CNV loss 17122850
esv3626855 CNV loss 21293372
esv993847 CNV deletion 20482838
nsv825996 CNV loss 20364138

Variation tolerance for GDPD5 Gene

Residual Variation Intolerance Score: 73.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.99; 36.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GDPD5 Gene

Human Gene Mutation Database (HGMD)
GDPD5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GDPD5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDPD5 Gene

Disorders for GDPD5 Gene

Additional Disease Information for GDPD5

No disorders were found for GDPD5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GDPD5 Gene

Publications for GDPD5 Gene

  1. Involvement of membrane protein GDE2 in retinoic acid-induced neurite formation in Neuro2A cells. (PMID: 17275818) Yanaka N … Kato N (FEBS letters 2007) 2 3 23 54
  2. Cloning and characterization of a human GDPD domain-containing protein GDPD5. (PMID: 17578682) Lang Q … Yu L (Molecular biology reports 2008) 3 23 54
  3. GDPD5 is a glycerophosphocholine phosphodiesterase that osmotically regulates the osmoprotective organic osmolyte GPC. (PMID: 18667693) Gallazzini M … Burg MB (Proceedings of the National Academy of Sciences of the United States of America 2008) 2 3 54
  4. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4 54
  5. Transmembrane protein GDE2 induces motor neuron differentiation in vivo. (PMID: 16195461) Rao M … Sockanathan S (Science (New York, N.Y.) 2005) 3 23 54

Products for GDPD5 Gene

Sources for GDPD5 Gene