PLPPR4 phospholipid phosphatase related 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLPPR4provided by HGNC
Official Full Name: phospholipid phosphatase related 4provided by HGNC
Primary source: HGNC:HGNC:23496
See related: Ensembl:ENSG00000117600 MIM:607813; AllianceGenome:HGNC:23496
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LPR4; PHP1; PRG1; LPPR4; PRG-1
Summary: The protein encoded by this gene belongs to the lipid phosphate phosphatase (LPP) family. LPPs catalyze the dephosphorylation of a number of bioactive lipid mediators that regulate a variety of cell functions. This protein is specifically expressed in neurons. It is located in the membranes of outgrowing axons and has been shown to be important for axonal outgrowth during development and regenerative sprouting. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]
Expression: Biased expression in brain (RPKM 35.4), testis (RPKM 3.7) and 2 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p21.3-p21.2

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (99262924..99309584)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (99111296..99157921)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (99730048..99775140)

Chromosome 1 - NC_000001.11 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?

PLPPR4 haploinsufficiency causes neurodevelopmental disorders by disrupting synaptic plasticity via mTOR signalling.
Title: PLPPR4 haploinsufficiency causes neurodevelopmental disorders by disrupting synaptic plasticity via mTOR signalling.
Glycosylation as a critical mechanism for PRG-1 function was significantly reduced by the PRG-1R346T SNP glycosylation as a critical mechanism
Title: Molecular cause and functional impact of altered synaptic lipid signaling due to a prg-1 gene SNP.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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
Association between liver-specific gene polymorphisms and their expression levels with nonalcoholic fatty liver disease. 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

SHGC-75185 (e-PCR)
- UniSTS:19517

A006O32 (e-PCR)
- UniSTS:54891

SHGC-75184 (e-PCR)
- UniSTS:42616

D1S3698 (e-PCR)
- UniSTS:474276

G34958 (e-PCR)
- UniSTS:117668

D1S2428 (e-PCR)
- UniSTS:10953

SHGC-75201 (e-PCR)
- UniSTS:41929

SHGC-75202 (e-PCR)
- UniSTS:37599

A009B28 (e-PCR)
- UniSTS:45822

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables lysophosphatidic acid phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidate phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidate phosphatase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
acts_upstream_of G protein-coupled receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in G protein-coupled receptor signaling pathway	TAS Traceable Author Statement more info
involved_in axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in inner ear development	IEA Inferred from Electronic Annotation more info
involved_in lipid import into cell	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in phospholipid dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of postsynapse organization	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic transmission, glutamatergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: phospholipid phosphatase-related protein type 4

Names: 2-lysophosphatidate phosphatase PLPPR4; brain-specific phosphatidic acid phosphatase-like protein 1; inactive 2-lysophosphatidate phosphatase PLPPR4; lipid phosphate phosphatase-related protein type 4; plasticity related gene 1; plasticity-related gene 1 protein

NP_001159724.2

EC 3.1.3.106

NP_055654.3

EC 3.1.3.106

XP_011540800.1

EC 3.1.3.106

XP_054195862.1

EC 3.1.3.106

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_001166252.2 → NP_001159724.2 phospholipid phosphatase-related protein type 4 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame coding exon in the 3' region, as compared to variant 1. The resulting isoform (2) is shorter and lacks an internal segment in the C-terminal region, as compared to isoform 1.

Source sequence(s)

AL136147, AL139425

Consensus CDS

CCDS53347.2

UniProtKB/TrEMBL

A0AAA9X798, B4DTT9

Related

ENSP00000394913.2, ENST00000457765.6

Conserved Domains (1) summary

cl00474
Location:126 → 219

PAP2_like; PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid ...
NM_014839.5 → NP_055654.3 phospholipid phosphatase-related protein type 4 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL136147, AL139425

Consensus CDS

CCDS757.2

UniProtKB/TrEMBL

Q86XM6

Related

ENSP00000359204.4, ENST00000370185.9

Conserved Domains (1) summary

cd03384
Location:126 → 275

PAP2_wunen; PAP2, wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system, which provides repellent activity towards primordial germ cells (PGCs), controls the ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

99262924..99309584

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011542498.3 → XP_011540800.1 phospholipid phosphatase-related protein type 4 isoform X1

See identical proteins and their annotated locations for XP_011540800.1

UniProtKB/TrEMBL

Q86XM6

Conserved Domains (1) summary

cd03384
Location:65 → 214

PAP2_wunen; PAP2, wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system, which provides repellent activity towards primordial germ cells (PGCs), controls the ...