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Aliases for GDPD1 Gene

Aliases for GDPD1 Gene

  • Glycerophosphodiester Phosphodiesterase Domain Containing 1 2 3 5
  • Glycerophosphodiester Phosphodiesterase Domain-Containing Protein 1 3 4
  • Glycerophosphodiester Phosphodiesterase 4 3 4
  • GDE4 3 4
  • Lysophospholipase D GDPD1 3
  • EC 3.1.4.39 4

External Ids for GDPD1 Gene

Previous GeneCards Identifiers for GDPD1 Gene

  • GC00U909461
  • GC17P054653
  • GC17P057297
  • GC17P052657

Summaries for GDPD1 Gene

Entrez Gene Summary for GDPD1 Gene

  • 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]

GeneCards Summary for GDPD1 Gene

GDPD1 (Glycerophosphodiester Phosphodiesterase Domain Containing 1) is a Protein Coding gene. Among its related pathways are Metabolism and PI 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 GDPD3.

UniProtKB/Swiss-Prot for GDPD1 Gene

  • Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylethanolamine (lyso-PE) and lysophosphatidylcholine (lyso-PC). May be involved in bioactive N-acylethanolamine biosynthesis. Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine.

Additional gene information for GDPD1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GDPD1 Gene

Genomics for GDPD1 Gene

GeneHancer (GH) Regulatory Elements for GDPD1 Gene

Promoters and enhancers for GDPD1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J059219 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.2 192 1.9 ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B ZNF207 GDPD1 TUBD1 HEATR6 RPS6KB1 SPDYE22P DHX40P1 TBC1D3P1 TBC1D3P1-DHX40P1 SETP3 NDUFB8P2
GH17J059209 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 0.4 -10.2 -10179 2.2 MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 SMG8 MKS1 TUBD1 RPS6KB1 NDUFB8P2 HEATR6 TRIM37 RNFT1 SKA2 DHX40
GH17J059123 Enhancer 0.4 FANTOM5 1.8 -97.3 -97265 0.1 ZNF121 ZNF362 GC17M059121 MIR301A SKA2 PRR11 SMG8 GDPD1 RNU2-58P
GH17J058924 Enhancer 0.3 FANTOM5 1.6 -296.0 -296029 0.2 CEBPG PPM1E SEPT4 GDPD1 ENSG00000275680 RPS12P30
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GDPD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GDPD1 gene promoter:
  • STAT3
  • Bach1
  • Nkx2-2
  • LyF-1
  • HNF-1A
  • HNF-1
  • AP-2gamma
  • ATF6
  • RSRFC4
  • HOXA9B

Genomic Locations for GDPD1 Gene

Genomic Locations for GDPD1 Gene
chr17:59,220,467-59,275,970
(GRCh38/hg38)
Size:
55,504 bases
Orientation:
Plus strand
chr17:57,297,828-57,353,331
(GRCh37/hg19)
Size:
55,504 bases
Orientation:
Plus strand

Genomic View for GDPD1 Gene

Genes around GDPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GDPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDPD1 Gene

Proteins for GDPD1 Gene

  • Protein details for GDPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N9F7-GDPD1_HUMAN
    Recommended name:
    Lysophospholipase D GDPD1
    Protein Accession:
    Q8N9F7
    Secondary Accessions:
    • A8W735
    • Q56VR1
    • Q8N4E3

    Protein attributes for GDPD1 Gene

    Size:
    314 amino acids
    Molecular mass:
    36167 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for GDPD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GDPD1 Gene

Post-translational modifications for GDPD1 Gene

  • Ubiquitination at isoforms=2, 341
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GDPD1 Gene

Domains & Families for GDPD1 Gene

Gene Families for GDPD1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for GDPD1 Gene

Suggested Antigen Peptide Sequences for GDPD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8N9F7

UniProtKB/Swiss-Prot:

GDPD1_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 GDPD1: view

Function for GDPD1 Gene

Molecular function for GDPD1 Gene

UniProtKB/Swiss-Prot Function:
Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylethanolamine (lyso-PE) and lysophosphatidylcholine (lyso-PC). May be involved in bioactive N-acylethanolamine biosynthesis. Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine.
UniProtKB/Swiss-Prot CatalyticActivity:
1-alkyl-sn-glycero-3-phosphoethanolamine + H(2)O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine.
UniProtKB/Swiss-Prot CatalyticActivity:
1-acyl-sn-glycero-3-phospho-(N-acyl)-ethanolamine + H(2)O = 1-acyl-sn-glycero-3-phosphate + N-acylethanolamine.
UniProtKB/Swiss-Prot CatalyticActivity:
1-acyl-sn-glycero-3-phosphoethanolamine + H(2)O = 1-acyl-sn-glycero-3-phosphate + ethanolamine.
UniProtKB/Swiss-Prot CatalyticActivity:
1-O-(alk-1Z-enyl)-sn-glycero-3-phospho-(N-acyl)-ethanolamine + H(2)O = 1-O-(1Z-alkenyl)-sn-glycero-3-phosphate + N-acylethanolamine.
UniProtKB/Swiss-Prot CatalyticActivity:
1-acyl-sn-glycero-3-phosphocholine + H(2)O = 1-acyl-sn-glycero-3-phosphate + choline.
UniProtKB/Swiss-Prot CatalyticActivity:
1-O-alkyl-sn-glycero-3-phosphocholine + H(2)O = 1-O-alkyl-sn-glycero-3-phosphate + choline.
UniProtKB/Swiss-Prot CatalyticActivity:
1-hexadecanoyl-sn-glycero-3-phosphocholine + H(2)O = 1-hexadecanoyl-sn-glycero-3-phosphate + choline.

Enzyme Numbers (IUBMB) for GDPD1 Gene

Phenotypes From GWAS Catalog for GDPD1 Gene

Gene Ontology (GO) - Molecular Function for GDPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004622 lysophospholipase activity IMP 25596343
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047391 alkylglycerophosphoethanolamine phosphodiesterase activity IEA --
genes like me logo Genes that share ontologies with GDPD1: view
genes like me logo Genes that share phenotypes with GDPD1: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GDPD1 Gene

Localization for GDPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDPD1 Gene

Cytoplasm. Membrane; Multi-pass membrane protein. Cytoplasm, perinuclear region. Note=Concentrated at the perinuclear region and the cell periphery (PubMed:18991142). {ECO:0000269 PubMed:18991142}.

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 GDPD1 gene
Compartment Confidence
plasma membrane 2
extracellular 2
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for GDPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
GO:0048471 perinuclear region of cytoplasm ISS --
genes like me logo Genes that share ontologies with GDPD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GDPD1 Gene

Pathways & Interactions for GDPD1 Gene

genes like me logo Genes that share pathways with GDPD1: view

Pathways by source for GDPD1 Gene

Gene Ontology (GO) - Biological Process for GDPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006644 phospholipid metabolic process IEA --
GO:0070291 N-acylethanolamine metabolic process IMP 25596343
genes like me logo Genes that share ontologies with GDPD1: view

No data available for SIGNOR curated interactions for GDPD1 Gene

Drugs & Compounds for GDPD1 Gene

No Compound Related Data Available

Transcripts for GDPD1 Gene

Unigene Clusters for GDPD1 Gene

Glycerophosphodiester phosphodiesterase domain containing 1:
Representative Sequences:

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GDPD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b
SP1: - -
SP2: - - -
SP3: -
SP4:

Relevant External Links for GDPD1 Gene

GeneLoc Exon Structure for
GDPD1
ECgene alternative splicing isoforms for
GDPD1

Expression for GDPD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GDPD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GDPD1 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x4.9).

Protein differential expression in normal tissues from HIPED for GDPD1 Gene

This gene is overexpressed in Adrenal (23.0), Fetal Brain (13.2), and Placenta (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GDPD1 Gene



Protein tissue co-expression partners for GDPD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GDPD1 Gene:

GDPD1

SOURCE GeneReport for Unigene cluster for GDPD1 Gene:

Hs.631744

mRNA Expression by UniProt/SwissProt for GDPD1 Gene:

Q8N9F7-GDPD1_HUMAN
Tissue specificity: Widely expressed with high expression level in testis.

Evidence on tissue expression from TISSUES for GDPD1 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with GDPD1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for GDPD1 Gene

Orthologs for GDPD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for GDPD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GDPD1 34
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GDPD1 34 33
  • 94.06 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GDPD1 34 33
  • 93.09 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gdpd1 33
  • 87.05 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GDPD1 34
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gdpd1 16 34 33
  • 86.94 (n)
oppossum
(Monodelphis domestica)
Mammalia GDPD1 34
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDPD1 34 33
  • 74.87 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GDPD1 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gdpd1 33
  • 73.01 (n)
Str.20315 33
zebrafish
(Danio rerio)
Actinopterygii gdpd1 34 33
  • 67.1 (n)
OneToOne
wufk14g09 33
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PGC1 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
OneToMany
Species where no ortholog for GDPD1 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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 GDPD1 Gene

ENSEMBL:
Gene Tree for GDPD1 (if available)
TreeFam:
Gene Tree for GDPD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GDPD1: view image

Paralogs for GDPD1 Gene

Paralogs for GDPD1 Gene

(1) SIMAP similar genes for GDPD1 Gene using alignment to 4 proteins:

  • GDPD1_HUMAN
  • J3KTA9_HUMAN
  • J3QQN7_HUMAN
  • J3QRR6_HUMAN
genes like me logo Genes that share paralogs with GDPD1: view

Variants for GDPD1 Gene

Sequence variations from dbSNP and Humsavar for GDPD1 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000053340 -- 59,270,528(+) G/A/T intron_variant
rs1000068923 -- 59,223,210(+) T/G genic_upstream_transcript_variant, intron_variant
rs1000093152 -- 59,255,550(+) T/C intron_variant
rs1000122213 -- 59,272,374(+) C/G intron_variant
rs1000177400 -- 59,230,468(+) C/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for GDPD1 Gene

Variant ID Type Subtype PubMed ID
nsv833500 CNV loss 17160897
nsv828070 CNV loss 20364138
nsv575804 CNV gain 21841781
nsv575803 CNV gain 21841781
nsv575802 CNV loss 21841781
nsv1138561 CNV deletion 24896259
nsv1109093 CNV deletion 24896259
nsv1065442 CNV gain 25217958
nsv1065063 CNV gain 25217958
nsv1062736 CNV gain 25217958
nsv1057152 CNV gain 25217958
esv3640903 CNV loss 21293372
esv3573764 CNV gain 25503493
esv2758699 CNV gain 17122850
dgv3271n100 CNV gain 25217958
dgv3270n100 CNV gain 25217958

Variation tolerance for GDPD1 Gene

Residual Variation Intolerance Score: 22.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.60; 12.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GDPD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GDPD1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDPD1 Gene

Disorders for GDPD1 Gene

Additional Disease Information for GDPD1

No disorders were found for GDPD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for GDPD1 Gene

Publications for GDPD1 Gene

  1. Isolation, characterization and molecular 3D model of human GDE4, a novel membrane protein containing glycerophosphodiester phosphodiesterase domain. (PMID: 18991142) Chang PA … Wu YJ (Molecular membrane biology 2008) 3 4 22 58
  2. Mammalian glycerophosphodiester phosphodiesterases. (PMID: 17690467) Yanaka N (Bioscience, biotechnology, and biochemistry 2007) 3 22 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. 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 58
  5. A novel splice variant of human gene GDPD1 is mainly expressed in human ovary and small intestine. (PMID: 14612981) Wu M … Mao Y (International journal of molecular medicine 2003) 2 3 58

Products for GDPD1 Gene

Sources for GDPD1 Gene

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