GDPD5 glycerophosphodiester phosphodiesterase domain containing 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: GDPD5provided by HGNC
Official Full Name: glycerophosphodiester phosphodiesterase domain containing 5provided by HGNC
Primary source: HGNC:HGNC:28804
See related: Ensembl:ENSG00000158555 MIM:609632; AllianceGenome:HGNC:28804
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: GDE2; PP1665
Summary: Predicted to enable glycerophosphocholine phosphodiesterase activity and phosphatidylinositol phospholipase C activity. Predicted to be involved in negative regulation of Notch signaling pathway and positive regulation of cell cycle. Predicted to act upstream of or within neuron differentiation; positive regulation of neuron differentiation; and regulation of timing of cell differentiation. Predicted to be located in membrane. Predicted to be part of axon; neuronal cell body; and perinuclear endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in spleen (RPKM 16.9), fat (RPKM 8.6) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.4-q13.5

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (75434640..75525941, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (75364149..75455494, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (75145685..75236986, complement)

Chromosome 11 - NC_000011.10 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

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?

Circ_0007142 downregulates miR-874-3p-mediated GDPD5 on colorectal cancer cells.
Title: Circ_0007142 downregulates miR-874-3p-mediated GDPD5 on colorectal cancer cells.
GDE2-RECK controls ADAM10 alpha-secretase-mediated cleavage of amyloid precursor protein.
Title: GDE2-RECK controls ADAM10 α-secretase-mediated cleavage of amyloid precursor protein.
Data suggest that GDE2/gdpd5 play roles in pancreatic organogenesis; gdpd5 knockdown leads to defects in differentiation of pancreas in zebrafish embryos; studies with recombinant fusion proteins suggest similar roles for homologous human GDE2 and zebrafish gdpd5.
Title: Glycerophosphodiesterase GDE2/GDPD5 affects pancreas differentiation in zebrafish.
miR-195-5p is a potent suppressor of GDPD5 and that, as such, it significantly increases chemosensitivity and apoptosis in chemoresistant colorectal cells.
Title: GDPD5, a target of miR-195-5p, is associated with metastasis and chemoresistance in colorectal cancer.
GDPD5 expression is strongly associated with favorable outcome in neuroblastoma. GDE2 induces differentiation of neuroblastoma cells, suppresses cell motility, and opposes RhoA-driven neurite retraction.
Title: Glycerophosphodiesterase GDE2 Promotes Neuroblastoma Differentiation through Glypican Release and Is a Marker of Clinical Outcome.
Identification of GDPD5 as a glycerophosphocholine phosphodiesterase that probably participates in the regulation of choline phospholipid metabolism in breast cancer.
Title: Glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5) expression correlates with malignant choline phospholipid metabolite profiles in human breast cancer.
GDPD5 was widely expressed in human tissues and the expression levels in kidney and prostate were relatively low
Title: Cloning and characterization of a human GDPD domain-containing protein GDPD5.

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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

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

D11S3866 (e-PCR)
- UniSTS:153089

AFMa135xf9 (e-PCR)
- UniSTS:73223

D11S4081 (e-PCR), detects polymorphism
- UniSTS:48415

AB046041 (e-PCR)
- UniSTS:480074

D11S1291 (e-PCR)
- UniSTS:68219

D11S534 (e-PCR)
- UniSTS:85643

A002S07 (e-PCR)
- UniSTS:30645

D11S1902 (e-PCR)
- UniSTS:37574

NIB1729 (e-PCR)
- UniSTS:12518

RH120771 (e-PCR)
- UniSTS:132851

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
located_in endomembrane system	IEA Inferred from Electronic Annotation more info
located_in growth cone	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

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Preferred Names: glycerophosphodiester phosphodiesterase domain-containing protein 5

Names: glycerophosphocholine phosphodiesterase GDPD5; glycerophosphodiester phosphodiesterase 2; phosphoinositide phospholipase C GDPD5

NP_001338096.1

EC 3.1.4.11

EC 3.1.4.2

NP_001338097.1

EC 3.1.4.11

EC 3.1.4.2

NP_110419.5

EC 3.1.4.11

EC 3.1.4.2

XP_006718760.1

EC 3.1.4.11

EC 3.1.4.2

XP_011543578.1

EC 3.1.4.11

EC 3.1.4.2

XP_011543579.1

EC 3.1.4.11

EC 3.1.4.2

XP_011543580.1

EC 3.1.4.11

EC 3.1.4.2

XP_011543582.1

EC 3.1.4.11

EC 3.1.4.2

XP_011543583.1

EC 3.1.4.11

EC 3.1.4.2

XP_011543588.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283601.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283602.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283603.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283604.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283605.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283606.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283607.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283608.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283609.1

EC 3.1.4.11

EC 3.1.4.2

XP_047283610.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226036.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226037.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226038.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226039.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226040.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226041.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226042.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226043.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226044.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226045.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226046.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226047.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226048.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226049.1

EC 3.1.4.11

EC 3.1.4.2

XP_054226050.1

EC 3.1.4.11

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_001351167.2 → NP_001338096.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' structure, resulting in a novel 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AP002815

Consensus CDS

CCDS86230.1

Related

ENSP00000434050.1, ENST00000526177.5

Conserved Domains (1) summary

cd08608
Location:89 → 438

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins
NM_001351168.1 → NP_001338097.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) contains an alternate exon, resulting in a novel 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AF318351, AP002815

Consensus CDS

CCDS86229.1

Related

ENSP00000435196.1, ENST00000533805.5

Conserved Domains (1) summary

cl14615
Location:1 → 331

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
NM_030792.8 → NP_110419.5 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 1

See identical proteins and their annotated locations for NP_110419.5

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AP002815

Consensus CDS

CCDS8238.1

UniProtKB/Swiss-Prot

Q8TB77, Q8WTR4

Related

ENSP00000337972.3, ENST00000336898.8

Conserved Domains (2) summary

cd08608
Location:227 → 576

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins

COG0584
Location:227 → 468

UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

75434640..75525941 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047427654.1 → XP_047283610.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_047427645.1 → XP_047283601.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1
XM_047427653.1 → XP_047283609.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_011545276.3 → XP_011543578.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

See identical proteins and their annotated locations for XP_011543578.1

Conserved Domains (2) summary

cd08608
Location:227 → 577

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins

COG0584
Location:227 → 468

UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
XM_047427649.1 → XP_047283605.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_047427646.1 → XP_047283602.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1
XM_006718697.4 → XP_006718760.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

See identical proteins and their annotated locations for XP_006718760.1

UniProtKB/Swiss-Prot

Q8TB77, Q8WTR4

Conserved Domains (2) summary

cd08608
Location:227 → 576

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins

COG0584
Location:227 → 468

UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
XM_047427652.1 → XP_047283608.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_011545278.3 → XP_011543580.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

See identical proteins and their annotated locations for XP_011543580.1

Conserved Domains (2) summary

cd08608
Location:227 → 577

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins

COG0584
Location:227 → 468

UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
XM_011545277.3 → XP_011543579.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

See identical proteins and their annotated locations for XP_011543579.1

Conserved Domains (2) summary

cd08608
Location:227 → 577

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins

COG0584
Location:227 → 468

UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
XM_047427648.1 → XP_047283604.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_047427650.1 → XP_047283606.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77

Related

ENSP00000433214.1, ENST00000529721.5
XM_047427651.1 → XP_047283607.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_047427647.1 → XP_047283603.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1
XM_011545280.2 → XP_011543582.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X3

Conserved Domains (2) summary

cd08608
Location:170 → 520

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins

COG0584
Location:170 → 411

UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
XM_011545281.3 → XP_011543583.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X4

See identical proteins and their annotated locations for XP_011543583.1

Related

ENSP00000437049.1, ENST00000533784.5

Conserved Domains (2) summary

cd08608
Location:89 → 439

GDPD_GDE2; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins

COG0584
Location:89 → 330

UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
XM_011545286.2 → XP_011543588.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X5

Conserved Domains (1) summary

cl14615
Location:1 → 332

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

75364149..75455494 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054370070.1 → XP_054226045.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370072.1 → XP_054226047.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370071.1 → XP_054226046.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370068.1 → XP_054226043.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370062.1 → XP_054226037.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1
XM_054370065.1 → XP_054226040.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370064.1 → XP_054226039.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1
XM_054370063.1 → XP_054226038.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1
XM_054370061.1 → XP_054226036.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1
XM_054370066.1 → XP_054226041.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370067.1 → XP_054226042.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370069.1 → XP_054226044.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q8TB77
XM_054370073.1 → XP_054226048.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X3
XM_054370074.1 → XP_054226049.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X4
XM_054370075.1 → XP_054226050.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X5