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

Summary

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, Dec 2024]
Expression: Broad expression in esophagus (RPKM 15.4), colon (RPKM 11.2) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p11.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (30104810..30113537, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (30387452..30396184, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (30116131..30124858, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MAPK3_2268 (e-PCR)
- UniSTS:280839

RH77963 (e-PCR)
- UniSTS:89158

SHGC-34253 (e-PCR)
- UniSTS:81524

G15873 (e-PCR)
- UniSTS:75694

SHGC-61070 (e-PCR)
- UniSTS:90564

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 more info	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)

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