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Aliases for GDPD3 Gene

Aliases for GDPD3 Gene

  • Glycerophosphodiester Phosphodiesterase Domain Containing 3 2 3 5
  • Glycerophosphodiester Phosphodiesterase Domain-Containing Protein 3 3
  • EC 3.1.-.- 4
  • GDE7 3

External Ids for GDPD3 Gene

Previous GeneCards Identifiers for GDPD3 Gene

  • GC16M030024
  • GC16M027777

Summaries for GDPD3 Gene

GeneCards Summary for GDPD3 Gene

GDPD3 (Glycerophosphodiester Phosphodiesterase Domain Containing 3) is a Protein Coding gene. Among its related pathways are Metabolism and Glycerophospholipid biosynthesis. GO annotations related to this gene include phosphoric diester hydrolase activity and glycerophosphodiester phosphodiesterase activity. An important paralog of this gene is GDPD1.

Additional gene information for GDPD3 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GDPD3 Gene

Genomics for GDPD3 Gene

Regulatory Elements for GDPD3 Gene

Enhancers for GDPD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16H030367 2 FANTOM5 Ensembl ENCODE dbSUPER 17.8 -262.1 -262090 17 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D ZNF610 GLIS1 SETD1A SRCAP INO80E NPIPB12 SMG1P5 SMG1P2 ZNF764 RNF40 ZNF747 ENSG00000260304
GH16H030566 2.1 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -455.9 -455932 6 ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A SETD1A SRCAP ENSG00000260267 ZNF747 NPIPB13 INO80E ZNF764 C16orf58 SMG1P5 SMG1P2
GH16H030074 1.3 ENCODE dbSUPER 13.5 +37.3 37259 4.6 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZHX2 REST ZNF592 KAT8 YPEL3 SRCAP SETD1A GDPD3 ZNF764 SMG1P5 ENSG00000198106 INO80E SMG1P2 NPIPB12
GH16H030052 1.4 ENCODE dbSUPER 11.3 +59.7 59739 3.1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 ZC3H11A SETD1A SRCAP INO80E NPIPB12 ZNF747 ZNF764 SMG1P5 SMG1P2 NPIPB13 BCL7C
GH16H030598 1.4 Ensembl ENCODE 11.2 -484.4 -484359 0.6 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF302 ZNF143 SP3 SRCAP INO80E ENSG00000260267 FBRS SETD1A ZNF764 PRR14 RNF40 SMG1P5 ENSG00000260304
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GDPD3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for GDPD3 Gene

Genomic Locations for GDPD3 Gene
9,134 bases
Minus strand

Genomic View for GDPD3 Gene

Genes around GDPD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDPD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GDPD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDPD3 Gene

Proteins for GDPD3 Gene

  • Protein details for GDPD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Glycerophosphodiester phosphodiesterase domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q9H652

    Protein attributes for GDPD3 Gene

    318 amino acids
    Molecular mass:
    36596 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH02714.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GDPD3 Gene


neXtProt entry for GDPD3 Gene

Post-translational modifications for GDPD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for GDPD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GDPD3 Gene

Domains & Families for GDPD3 Gene

Gene Families for GDPD3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for GDPD3 Gene

Suggested Antigen Peptide Sequences for GDPD3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
genes like me logo Genes that share domains with GDPD3: view

Function for GDPD3 Gene

Enzyme Numbers (IUBMB) for GDPD3 Gene

Phenotypes From GWAS Catalog for GDPD3 Gene

Gene Ontology (GO) - Molecular Function for GDPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with GDPD3: view
genes like me logo Genes that share phenotypes with GDPD3: view

Clone Products

No data available for Molecular function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for GDPD3 Gene

Localization for GDPD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDPD3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

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 GDPD3 gene
Compartment Confidence
extracellular 5
mitochondrion 2
nucleus 2
cytosol 2
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (2)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GDPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005789 endoplasmic reticulum membrane ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0048471 perinuclear region of cytoplasm ISS --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with GDPD3: view

Pathways & Interactions for GDPD3 Gene

genes like me logo Genes that share pathways with GDPD3: view

Gene Ontology (GO) - Biological Process for GDPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034638 phosphatidylcholine catabolic process IEA --
genes like me logo Genes that share ontologies with GDPD3: view

No data available for SIGNOR curated interactions for GDPD3 Gene

Drugs & Compounds for GDPD3 Gene

No Compound Related Data Available

Transcripts for GDPD3 Gene

Unigene Clusters for GDPD3 Gene

Glycerophosphodiester phosphodiesterase domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GDPD3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c
SP1: -
SP4: -

Relevant External Links for GDPD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for GDPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GDPD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GDPD3 Gene

This gene is overexpressed in Esophagus - Mucosa (x5.9).

Protein differential expression in normal tissues from HIPED for GDPD3 Gene

This gene is overexpressed in Urine (27.7), Cervix (22.2), and Lung (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GDPD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of GDPD3 Gene:


SOURCE GeneReport for Unigene cluster for GDPD3 Gene:


Evidence on tissue expression from TISSUES for GDPD3 Gene

  • Intestine(4.1)
genes like me logo Genes that share expression patterns with GDPD3: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GDPD3 Gene

Orthologs for GDPD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for GDPD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia GDPD3 33 34
  • 99.48 (n)
(Bos Taurus)
Mammalia GDPD3 33 34
  • 84.7 (n)
(Canis familiaris)
Mammalia GDPD3 33 34
  • 83.86 (n)
(Mus musculus)
Mammalia Gdpd3 33 16 34
  • 81.49 (n)
(Rattus norvegicus)
Mammalia Gdpd3 33
  • 80.71 (n)
(Monodelphis domestica)
Mammalia GDPD3 34
  • 73 (a)
(Ornithorhynchus anatinus)
Mammalia GDPD3 34
  • 59 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100125107 33
  • 56.32 (n)
(Danio rerio)
Actinopterygii gdpd3b 33 34
  • 55.18 (n)
gdpd3a 34
  • 47 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
Species where no ortholog for GDPD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 GDPD3 Gene

Gene Tree for GDPD3 (if available)
Gene Tree for GDPD3 (if available)

Paralogs for GDPD3 Gene

Paralogs for GDPD3 Gene

(1) SIMAP similar genes for GDPD3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with GDPD3: view

Variants for GDPD3 Gene

Sequence variations from dbSNP and Humsavar for GDPD3 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000228969 -- 30,107,161(+) AGTGG(C/T)GTGAT intron-variant
rs1000632261 -- 30,111,910(+) CCTGG(A/G)CGACA intron-variant
rs1000703831 -- 30,110,378(+) GTGAG(A/C)CGAGA intron-variant
rs1000737377 -- 30,111,692(+) GTTTG(C/G)GAGGC intron-variant
rs1001796639 -- 30,111,077(+) GGACC(C/T)CTCCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for GDPD3 Gene

Variant ID Type Subtype PubMed ID
nsv833187 CNV loss 17160897
nsv1160384 CNV duplication 26073780
nsv1131237 CNV deletion 24896259
esv2758642 CNV gain 17122850

Variation tolerance for GDPD3 Gene

Residual Variation Intolerance Score: 81.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.76; 47.00% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for GDPD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDPD3 Gene

Disorders for GDPD3 Gene

Relevant External Links for GDPD3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for GDPD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GDPD3 Gene

Publications for GDPD3 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  4. Biological insights from 108 schizophrenia-associated genetic loci. (PMID: 25056061) Schizophrenia Working Group of the Psychiatric Genomics Consortium (Nature 2014) 3 60
  5. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M … Moll S (Journal of proteomics 2013) 3 60

Products for GDPD3 Gene

Sources for GDPD3 Gene

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