GDPD3 (glycerophosphodiester phosphodiesterase domain containing 3)

Gene

• Entrez ID: 79153
• Gene name: Glycerophosphodiester phosphodiesterase domain containing 3
• Gene symbol: GDPD3
• Synonyms (NCBI Gene): GDE7
• Chromosome: 16
• Chromosome location: 16p11.2

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1016052	hsa-miR-873	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004622	Function	Phosphatidylcholine lysophospholipase activity	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	IMP	27637550
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	ISS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006644	Process	Phospholipid metabolic process	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IBA
GO:0008081	Function	Phosphoric diester hydrolase activity	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IMP	27637550
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0034638	Process	Phosphatidylcholine catabolic process	IEA
GO:0046475	Process	Glycerophospholipid catabolic process	IBA
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	ISS
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0070291	Process	N-acylethanolamine metabolic process	IEA
GO:0070291	Process	N-acylethanolamine metabolic process	IMP	27637550

Other IDs

• MIM: 616318
• HGNC: 28638
• e!Ensembl: ENSG00000102886

Protein

• UniProt ID: Q7L5L3
• Protein name: Lysophospholipase D GDPD3 (EC 3.1.4.-) (Glycerophosphodiester phosphodiesterase 7) (Glycerophosphodiester phosphodiesterase domain-containing protein 3)
• Protein function: Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines (PubMed:27637550). Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylcholine (lyso-PC) and N-acylethan
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03009	GDPD	44 → 303	Glycerophosphoryl diester phosphodiesterase family	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed, with high level in kidney and ovary. {ECO:0000269|PubMed:27637550}.
• Sequence:

  MSLLLYYALPALGSYAMLSIFFLRRPHLLHTPRAPTFRIRLGAHRGGSGELLENTMEAME
  NSMAQRSDLLELDCQLTRDRVVVVSHDENLCRQSGLNRDVGSLDFEDLPLYKEKLEVYFS
  PGHFAHGSDRRMVRLEDLFQRFPRTPMSVEIKGKNEELIREIAGLVRRYDRNEITIWASE
  KSSVMKKCKAANPEMPLSFTISRGFWVLLSYYLGLLPFIPIPEKFFFCFLPNIINRTYFP
  FSCSCLNQLLAVVSKWLIMRKSLIRHLEERGVQVVFWCLNEESDFEAAFSVGATGVITDY
  PTALRHYLDNHGPAARTS

• Sequence length: 318

Pathways

KEGG:

Ether lipid metabolism
Metabolic pathways

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
LIPIDOSES	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIPOIDOSIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Lipoidosis	Lipoidosis	CTD_human_DG	15342952, 16919414, 17175557		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28522585		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	28522585, 30186285		★☆☆☆☆ Found in Text Mining only