GPCPD1 glycerophosphocholine phosphodiesterase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: GPCPD1provided by HGNC
Official Full Name: glycerophosphocholine phosphodiesterase 1provided by HGNC
Primary source: HGNC:HGNC:26957
See related: Ensembl:ENSG00000125772 MIM:614124; AllianceGenome:HGNC:26957
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: EDI3; GDE5; GDPD6; PREI4
Summary: Predicted to enable glycerophosphocholine phosphodiesterase activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within skeletal muscle tissue development. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in bone marrow (RPKM 31.5), spleen (RPKM 13.3) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20p12.3

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (5544439..5611006, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (5585120..5651341, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (5525085..5591652, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

EDI3 knockdown in ER-HER2+ breast cancer cells reduces tumor burden and improves survival in two mouse models of experimental metastasis.
Title: EDI3 knockdown in ER-HER2+ breast cancer cells reduces tumor burden and improves survival in two mouse models of experimental metastasis.
Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism.
Title: Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism.
Hypoxia-induced GPCPD1 depalmitoylation triggers mitophagy via regulating PRKN-mediated ubiquitination of VDAC1.
Title: Hypoxia-induced GPCPD1 depalmitoylation triggers mitophagy via regulating PRKN-mediated ubiquitination of VDAC1.
Inhibiting the glycerophosphodiesterase EDI3 in ER-HER2+ breast cancer cells resistant to HER2-targeted therapy reduces viability and tumour growth.
Title: Inhibiting the glycerophosphodiesterase EDI3 in ER-HER2+ breast cancer cells resistant to HER2-targeted therapy reduces viability and tumour growth.
Circular RNA circSNX6 promotes sunitinib resistance in renal cell carcinoma through the miR-1184/GPCPD1/ lysophosphatidic acid axis.
Title: Circular RNA circSNX6 promotes sunitinib resistance in renal cell carcinoma through the miR-1184/GPCPD1/ lysophosphatidic acid axis.
EDI3 links choline metabolism to integrin expression, cell adhesion and spreading
Title: EDI3 links choline metabolism to integrin expression, cell adhesion and spreading.
We have identified EDI3, a key enzyme controlling GPC and choline metabolism; Because inhibition of it corrects the GPC/PC ratio and decreases the migration capacity of tumor cells, it represents a possible target for therapeutic intervention.
Title: Choline-releasing glycerophosphodiesterase EDI3 drives tumor cell migration and metastasis.
common genetic variants in GPCPD1 are associated with scaling of visual cortical surface area in humans
Title: Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans. 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

RH103206 (e-PCR)
- UniSTS:97539

MARC_12069-12070:1004549810:1 (e-PCR)
- UniSTS:267327

STS-R10161 (e-PCR)
- UniSTS:38524

D20S760 (e-PCR)
- UniSTS:53121

EST159813 (e-PCR)
- UniSTS:80778

RH64148 (e-PCR)
- UniSTS:68251

Z94598 (e-PCR)
- UniSTS:19868

STS-R79720 (e-PCR)
- UniSTS:24786

WI-20801 (e-PCR)
- UniSTS:3798

RH70786 (e-PCR)
- UniSTS:67810

WI-17673 (e-PCR)
- UniSTS:37876

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables glycerophosphocholine phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables starch binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in glycerophospholipid catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal muscle tissue development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: glycerophosphocholine phosphodiesterase GPCPD1

Names: endometrial differential 3; glycerophosphocholine phosphodiesterase GDE1 homolog; glycerophosphodiester phosphodiesterase 5; preimplantation protein 4; putative glycerophosphocholine phosphodiesterase GPCPD1; putative glycerophosphodiester phosphodiesterase 5

NP_062539.1

EC 3.1.4.2

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_019593.5 → NP_062539.1 glycerophosphocholine phosphodiesterase GPCPD1

See identical proteins and their annotated locations for NP_062539.1

Status: VALIDATED

Source sequence(s)

AB037855, AL049446, BC027588, BG674365, BI561344, BP421674, T79323

Consensus CDS

CCDS13090.1

UniProtKB/Swiss-Prot

D3DW06, Q9BQL8, Q9NPB8, Q9NUX0

Related

ENSP00000368305.4, ENST00000379019.7

Conserved Domains (2) summary

cd05814
Location:4 → 127

CBM20_Prei4; Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 ...

cd08607
Location:319 → 611

GDPD_GDE5; Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins