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

Gene ID: 79153, updated on 5-Mar-2024

Summary

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Official Symbol
GDPD3provided by HGNC
Official Full Name
glycerophosphodiester phosphodiesterase domain containing 3provided by HGNC
Primary source
HGNC:HGNC:28638
See related
Ensembl:ENSG00000102886 MIM:616318; AllianceGenome:HGNC:28638
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GDE7
Summary
Enables phosphoric diester hydrolase activity. Involved in N-acylethanolamine metabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in esophagus (RPKM 15.4), colon (RPKM 11.2) and 22 other tissues See more
Orthologs
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Genomic context

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See GDPD3 in Genome Data Viewer
Location:
16p11.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30104810..30113537, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30387452..30396184, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30116131..30124858, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30101709-30102582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30107354-30107960 Neighboring gene T-box transcription factor 6 Neighboring gene YPEL3 divergent transcript Neighboring gene yippee like 3 Neighboring gene Sharpr-MPRA regulatory region 9068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7356 Neighboring gene mitogen-activated protein kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30187986-30188486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195204-30195744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30195745-30196286 Neighboring gene CORO1A antisense RNA 1 Neighboring gene coronin 1A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Human GDPD3 overexpression promotes liver steatosis by increasing lysophosphatidic acid production and fatty acid uptake. Key CC, et al. J Lipid Res, 2020 Jul. PMID 32430316, Free PMC Article
  2. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7. Kitakaze K, et al. J Lipid Res, 2021. PMID 34673020, Free PMC Article
  3. Calcium-dependent generation of N-acylethanolamines and lysophosphatidic acids by glycerophosphodiesterase GDE7. Rahman IA, et al. Biochim Biophys Acta, 2016 Dec. PMID 27637550
  4. A pancreatic cancer-specific expression profile. Gress TM, et al. Oncogene, 1996 Oct 17. PMID 8895530
  5. Biological insights from 108 schizophrenia-associated genetic loci. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Nature, 2014 Jul 24. PMID 25056061, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GDE7 produces cyclic phosphatidic acid in the ER lumen functioning as a lysophospholipid mediator.
    Title: GDE7 produces cyclic phosphatidic acid in the ER lumen functioning as a lysophospholipid mediator.
  2. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7.
    Title: Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7.
  3. Human GDPD3 overexpression promotes liver steatosis by increasing lysophosphatidic acid production and fatty acid uptake.
    Title: Human GDPD3 overexpression promotes liver steatosis by increasing lysophosphatidic acid production and fatty acid uptake.
Submit: New GeneRIF Correction

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC4171, FLJ22603

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables lysophospholipase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphoric diester hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphoric diester hydrolase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in N-acylethanolamine metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in glycerophospholipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phosphatidylcholine catabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in extracellular exosome HDA PubMed 
located_in perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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

NCBI Reference Sequences (RefSeq)

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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_024307.3 → NP_077283.2  lysophospholipase D GDPD3

    See identical proteins and their annotated locations for NP_077283.2

    Status: VALIDATED

    Source sequence(s)
    BC002714
    Consensus CDS
    CCDS10671.2
    UniProtKB/Swiss-Prot
    Q7L5L3, Q9H652
    Related
    ENSP00000384363.3, ENST00000406256.8
    Conserved Domains (2) summary
    cd08612
    Location:13 → 310
    GDPD_GDE4; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins
    pfam03009
    Location:44 → 301
    GDPD; Glycerophosphoryl diester phosphodiesterase family

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    30104810..30113537 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_007064912.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    30387452..30396184 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7L5L3.3 GenPept UniProtKB/Swiss-Prot:Q7L5L3

Gene LinkOut

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

Chemical Information
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