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GDPD3 glycerophosphodiester phosphodiesterase domain containing 3 [ Homo sapiens (human) ]

Gene ID: 79153, updated on 17-Nov-2018


Official Symbol
GDPD3provided by HGNC
Official Full Name
glycerophosphodiester phosphodiesterase domain containing 3provided by HGNC
Primary source
See related
Ensembl:ENSG00000102886 MIM:616318; Vega:OTTHUMG00000132106
Gene type
protein coding
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Broad expression in esophagus (RPKM 15.4), colon (RPKM 11.2) and 22 other tissues See more

Genomic context

See GDPD3 in Genome Data Viewer
Exon count:
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (30104810..30113557, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30115977..30125264, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928595 Neighboring gene T-box 6 Neighboring gene yippee like 3 Neighboring gene mitogen-activated protein kinase 3 Neighboring gene uncharacterized LOC107984834 Neighboring gene coronin 1A

Genomic regions, transcripts, and products


  • 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 Jun 15 11:32:44 2016


Related articles in PubMed

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Glycerophospholipid catabolism, organism-specific biosystem (from REACTOME)
    Glycerophospholipid catabolism, organism-specific biosystemReactions grouped in this pathway because of their shared chemistry - the hydrolysis of various phosphatidyl inositols and related phospholipids. They differ, however, in the tissues in which they oc...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • PI Metabolism, organism-specific biosystem (from REACTOME)
    PI Metabolism, organism-specific biosystemPhosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phos...
  • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
    Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...


Products Interactant Other Gene Complex Source Pubs Description

General gene information



Clone Names

  • MGC4171, FLJ22603

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
phosphoric diester hydrolase activity IEA
Inferred from Electronic Annotation
more info
Process Evidence Code Pubs
phosphatidylcholine catabolic process IEA
Inferred from Electronic Annotation
more info
Component Evidence Code Pubs
endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
extracellular exosome HDA PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info

General protein information

Preferred Names
lysophospholipase D GDPD3
glycerophosphodiester phosphodiesterase 7
glycerophosphodiester phosphodiesterase domain-containing protein 3

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_024307.2NP_077283.2  lysophospholipase D GDPD3

    See identical proteins and their annotated locations for NP_077283.2

    Status: VALIDATED

    Source sequence(s)
    Consensus CDS
    ENSP00000384363.3, OTTHUMP00000162982, ENST00000406256.7, OTTHUMT00000255144
    Conserved Domains (2) summary
    GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins
    GDPD; Glycerophosphoryl diester phosphodiesterase family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly


  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    30104810..30113557 complement
    GenBank, FASTA, Sequence Viewer (Graphics)
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