PLPPR4

gene
On this page

Also known as PRG-1LPPR4KIAA0455PHP1

Summary

PLPPR4 (phospholipid phosphatase related 4, HGNC:23496) is a protein-coding gene on chromosome 1p21.3-p21.2, encoding Phospholipid phosphatase-related protein type 4 (Q7Z2D5). Postsynaptic density membrane protein that indirectly regulates glutamatergic synaptic transmission through lysophosphatidic acid (LPA)-mediated signaling pathways.

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.

Source: NCBI Gene 9890 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 47 total
  • MANE Select transcript: NM_014839

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23496
Approved symbolPLPPR4
Namephospholipid phosphatase related 4
Location1p21.3-p21.2
Locus typegene with protein product
StatusApproved
AliasesPRG-1, LPPR4, KIAA0455, PHP1
Ensembl geneENSG00000117600
Ensembl biotypeprotein_coding
OMIM607813
Entrez9890

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000370184, ENST00000370185, ENST00000457765, ENST00000917620, ENST00000917621

RefSeq mRNA: 2 — MANE Select: NM_014839 NM_001166252, NM_014839

CCDS: CCDS53347, CCDS757

Canonical transcript exons

ENST00000370185 — 7 exons

ExonStartEnd
ENSE000007776069930172499301897
ENSE000007776099929903599299230
ENSE000008312489930090999300966
ENSE000010033919928796599288150
ENSE000010670789929673899296867
ENSE000014520209930568599309584
ENSE000018771929926449299264671

Expression profiles

Bgee: expression breadth ubiquitous, 213 present calls, max score 97.63.

FANTOM5 (CAGE): breadth broad, TPM avg 5.4219 / max 385.5303, expressed in 405 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
41662.7556276
41651.9345259
41630.6099104
41670.069948
41690.035117
41680.017010

Top tissues by expression

286 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
CA1 field of hippocampusUBERON:000388197.63gold quality
orbitofrontal cortexUBERON:000416796.60gold quality
entorhinal cortexUBERON:000272895.93gold quality
Brodmann (1909) area 23UBERON:001355495.60gold quality
cortical plateUBERON:000534394.64gold quality
superior frontal gyrusUBERON:000266192.97gold quality
endothelial cellCL:000011592.81gold quality
Brodmann (1909) area 46UBERON:000648392.67gold quality
middle temporal gyrusUBERON:000277191.88gold quality
prefrontal cortexUBERON:000045191.69gold quality
frontal poleUBERON:000279590.55gold quality
parietal lobeUBERON:000187290.51gold quality
postcentral gyrusUBERON:000258190.51gold quality
Ammon’s hornUBERON:000195490.43gold quality
temporal lobeUBERON:000187190.16gold quality
frontal cortexUBERON:000187089.85gold quality
primary visual cortexUBERON:000243689.80gold quality
cerebral cortexUBERON:000095689.78gold quality
occipital lobeUBERON:000202189.47gold quality
neocortexUBERON:000195089.23gold quality
dorsolateral prefrontal cortexUBERON:000983489.11gold quality
nucleus accumbensUBERON:000188288.94gold quality
Brodmann (1909) area 9UBERON:001354088.82gold quality
Brodmann (1909) area 10UBERON:001354188.48gold quality
telencephalonUBERON:000189388.47gold quality
lateral nuclear group of thalamusUBERON:000273687.65gold quality
forebrainUBERON:000189087.61gold quality
amygdalaUBERON:000187686.71gold quality
cingulate cortexUBERON:000302786.34gold quality
ventricular zoneUBERON:000305386.34gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

206 targeting PLPPR4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-4682100.0068.891258
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3646100.0073.565283
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-188-3P100.0068.761240
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-186-5P99.9970.833707
HSA-MIR-318599.9968.121959
HSA-MIR-548AW99.9972.573559
HSA-MIR-366299.9973.825684
HSA-MIR-1213699.9872.815713
HSA-MIR-548P99.9872.253784
HSA-MIR-23B-5P99.9866.07587
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-477599.9875.006394
HSA-MIR-314899.9775.066478

Literature-anchored findings (GeneRIF, showing 2)

  • Glycosylation as a critical mechanism for PRG-1 function was significantly reduced by the PRG-1R346T SNP glycosylation as a critical mechanism (PMID:26671989)
  • PLPPR4 haploinsufficiency causes neurodevelopmental disorders by disrupting synaptic plasticity via mTOR signalling. (PMID:37550884)

Cross-species orthologs

13 orthologs

OrganismSymbolGene ID
danio_rerioplppr4bENSDARG00000078755
danio_rerioplppr4aENSDARG00000079671
mus_musculusPlppr4ENSMUSG00000044667
rattus_norvegicusPlppr4ENSRNOG00000016872
drosophila_melanogasterwunFBGN0016078
drosophila_melanogasterlazaFBGN0037163
drosophila_melanogasterCG11438FBGN0037164
drosophila_melanogasterCG11437FBGN0037165
drosophila_melanogasterCG11426FBGN0037166
drosophila_melanogasterCG11425FBGN0037167
drosophila_melanogasterCG12746FBGN0037341
drosophila_melanogasterwun2FBGN0041087
caenorhabditis_elegansWBGENE00018756

Paralogs (9): PLPP1 (ENSG00000067113), PLPPR2 (ENSG00000105520), PLPPR5 (ENSG00000117598), PLPPR3 (ENSG00000129951), PLPP2 (ENSG00000141934), PLPP5 (ENSG00000147535), PLPPR1 (ENSG00000148123), PLPP3 (ENSG00000162407), PLPP4 (ENSG00000203805)

Protein

Protein identifiers

Phospholipid phosphatase-related protein type 4Q7Z2D5 (reviewed: Q7Z2D5)

Alternative names: Brain-specific phosphatidic acid phosphatase-like protein 1, Inactive 2-lysophosphatidate phosphatase PLPPR4, Lipid phosphate phosphatase-related protein type 4, Plasticity-related gene 1 protein

All UniProt accessions (2): Q7Z2D5, A0AAA9X798

UniProt curated annotations — full annotation on UniProt →

Function. Postsynaptic density membrane protein that indirectly regulates glutamatergic synaptic transmission through lysophosphatidic acid (LPA)-mediated signaling pathways. Binds lysophosphatidic acid (LPA) and mediates its internalization into cells. Could act as receptor or a transporter of this lipid at the post-synaptic membrane. Modulates lysophosphatidic acid (LPA) activity in neuron axonal outgrowth during development by attenuating phospholipid-induced axon collapse.

Subcellular location. Postsynaptic density membrane.

Tissue specificity. Expressed by glutamatergic neurons (at protein level).

Post-translational modifications. O-glycosylated. Probably at Ser-346.

Similarity. Belongs to the PA-phosphatase related phosphoesterase family.

Isoforms (4)

UniProt IDNamesCanonical?
Q7Z2D5-11yes
Q7Z2D5-22
Q7Z2D5-33
Q7Z2D5-44

RefSeq proteins (2): NP_001159724, NP_055654* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000326PAP2/HPODomain
IPR036938PAP2/HPO_sfHomologous_superfamily
IPR043216PAP-likeFamily

Pfam: PF01569

Enzyme classification (BRENDA):

  • EC 3.1.3.4 — phosphatidate phosphatase (BRENDA: 31 organisms, 190 substrates, 196 inhibitors, 44 Km, 3 kcat entries)

Substrate kinetics (BRENDA)

10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
PHOSPHATIDIC ACID0.0054–1.217
LYSOPHOSPHATIDATE0.046–0.1793
PHOSPHATIDATE0.284–0.3693
SPHINGOSINE-1-PHOSPHATE0.028–0.263
CERAMIDE-1-PHOSPHATE0.022–0.0522
DIACYLGLYCEROL DIPHOSPHATE0.041–0.1042
LYSOPHOSPHATIDIC ACID0.295–0.582
1,2-DIACYL-SN-GLYCEROL-3-PHOSPHATE0.59541
2-(4,4-DIFLUORO-5,7-DIMETHYL-4-BORA-3A,4A-DIAZA-0.0241
DIOCTANOYL PHOSPHATIDIC ACID1.41

UniProt features (39 total): glycosylation site 9, modified residue 7, transmembrane region 6, region of interest 4, splice variant 4, sequence variant 4, compositionally biased region 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7Z2D5-F156.090.19

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (7): 36, 346, 385, 438, 461, 472, 606

Glycosylation sites (9): 214, 219, 268, 362, 432, 455, 513, 543, 568

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-419408Lysosphingolipid and LPA receptors

MSigDB gene sets: 229 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GOBP_LIPID_MODIFICATION, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, JAEGER_METASTASIS_DN, GOBP_REGULATION_OF_SYNAPTIC_TRANSMISSION_GLUTAMATERGIC, GOBP_PHOSPHOLIPID_DEPHOSPHORYLATION, TATTATA_MIR374, GOBP_NEUROGENESIS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, MORF_RAD51L3, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_EAR_DEVELOPMENT, MORF_CTSB

GO Biological Process (9): phospholipid metabolic process (GO:0006644), signal transduction (GO:0007165), G protein-coupled receptor signaling pathway (GO:0007186), axonogenesis (GO:0007409), inner ear development (GO:0048839), regulation of synaptic transmission, glutamatergic (GO:0051966), regulation of postsynapse organization (GO:0099175), lipid import into cell (GO:0140354), modulation of chemical synaptic transmission (GO:0050804)

GO Molecular Function (1): phosphatidate phosphatase activity (GO:0008195)

GO Cellular Component (7): plasma membrane (GO:0005886), Schaffer collateral - CA1 synapse (GO:0098685), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), membrane (GO:0016020), synapse (GO:0045202), postsynaptic membrane (GO:0045211)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Class A/1 (Rhodopsin-like receptors)1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
synapse2
lipid metabolic process1
organophosphate metabolic process1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
G protein-coupled receptor activity1
signal transduction1
cell morphogenesis involved in neuron differentiation1
neuron projection morphogenesis1
axon development1
ear development1
anatomical structure development1
synaptic transmission, glutamatergic1
modulation of chemical synaptic transmission1
regulation of synapse organization1
postsynapse organization1
lipid transport1
chemical synaptic transmission1
regulation of trans-synaptic signaling1
lipid phosphatase activity1
membrane1
cell periphery1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1
cellular anatomical structure1
cell junction1
synaptic membrane1
postsynapse1

Protein interactions and networks

STRING

1072 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PLPPR4EPHX2P34913739
PLPPR4GNASQ5JWF2570
PLPPR4MCF2L2Q86YR7502
PLPPR4PTHP01270500
PLPPR4LPAR2Q9HBW0448
PLPPR4SLC38A8A6NNN8446
PLPPR4STX16O14662423
PLPPR4PALMDQ9NP74413
PLPPR4CALM1P02593406
PLPPR4PIP4P2Q8N4L2404
PLPPR4CALML6Q8TD86399
PLPPR4CALML4Q96GE6399
PLPPR4CALML3P27482398
PLPPR4CALML5Q9NZT1398
PLPPR4SPDYE16A6NNV3397

IntAct

6 interactions, top by confidence:

ABTypeScore
NPAP1ACACBpsi-mi:“MI:0914”(association)0.350
DESI1HRASpsi-mi:“MI:0914”(association)0.350
ZNRF3ITGA8psi-mi:“MI:0914”(association)0.350
PLPPR4FAM91A1psi-mi:“MI:0914”(association)0.350
PLPPR1TNFRSF10Bpsi-mi:“MI:0914”(association)0.350

BioGRID (12): LPPR4 (Two-hybrid), TRIM67 (Affinity Capture-Western), TRIM9 (Affinity Capture-Western), NDUFAF7 (Affinity Capture-MS), FAM91A1 (Affinity Capture-MS), PVRL2 (Affinity Capture-MS), LPPR4 (Affinity Capture-MS), DCAKD (Affinity Capture-MS), LPPR4 (Affinity Capture-MS), MIB2 (Affinity Capture-MS), LPPR4 (Affinity Capture-MS), LPPR4 (Affinity Capture-MS)

ESM2 similar proteins: A0JPH4, A3KGS3, A4IG66, A9ZLX4, F1M8G0, F1Q930, H2MCM1, O17482, O23693, O54828, O95772, P49021, P49805, P86411, Q08DA4, Q17QW2, Q28C33, Q28EW0, Q3B7T1, Q3UD82, Q4QQM5, Q5R9R1, Q5VW38, Q5YLM1, Q5ZKN3, Q66H44, Q6GQV7, Q6WQJ1, Q7Z2D5, Q7ZW11, Q7ZYA0, Q810L4, Q8AVJ1, Q8BKU8, Q8BUV8, Q8BXN9, Q8CB19, Q8IY22, Q8N3A8, Q8N3S3

Diamond homologs: A4II83, Q29RT8, Q32ZL2, Q3SZE3, Q6GM05, Q6GQ62, Q6IQH6, Q6T4P5, Q6W5G4, Q6WAY2, Q7TMB0, Q7TMB7, Q7TME0, Q7TPB0, Q7Z2D5, Q8BFZ2, Q8BJ52, Q8TBJ4, Q8VCY8, Q96GM1, O08564, O14494, O14495, O43688, O88956, P60588, P97544, Q04396, Q0WNG6, Q10022, Q2HJ61, Q3UMZ3, Q54PR7, Q61469, Q8K593, Q8LFD1, Q8NEB5, Q99JY8, Q9DAX2, Q9V576

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

47 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance38
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

923 predictions. Top by Δscore:

VariantEffectΔscore
1:99287963:A:AGacceptor_gain1.0000
1:99287964:G:GGacceptor_gain1.0000
1:99296860:A:Gdonor_gain1.0000
1:99299032:TA:Tacceptor_loss1.0000
1:99299033:A:AGacceptor_gain1.0000
1:99299033:A:Cacceptor_loss1.0000
1:99299034:G:GAacceptor_loss1.0000
1:99299034:G:GGacceptor_gain1.0000
1:99299034:GGT:Gacceptor_gain1.0000
1:99299228:CAGG:Cdonor_loss1.0000
1:99299229:AG:Adonor_loss1.0000
1:99299230:GG:Gdonor_loss1.0000
1:99299231:G:Cdonor_loss1.0000
1:99300903:T:TAacceptor_gain1.0000
1:99300907:A:AGacceptor_gain1.0000
1:99300908:G:GGacceptor_gain1.0000
1:99300908:GA:Gacceptor_gain1.0000
1:99300908:GAA:Gacceptor_gain1.0000
1:99300908:GAAA:Gacceptor_gain1.0000
1:99300964:TCGGT:Tdonor_loss1.0000
1:99300966:GGTA:Gdonor_loss1.0000
1:99300967:G:GGdonor_gain1.0000
1:99300968:TAA:Tdonor_loss1.0000
1:99301722:A:Gacceptor_gain1.0000
1:99301723:GAT:Gacceptor_gain1.0000
1:99301831:G:GGdonor_gain1.0000
1:99285187:A:Gdonor_gain0.9900
1:99287235:GCAT:Gdonor_gain0.9900
1:99287964:GT:Gacceptor_gain0.9900
1:99287964:GTT:Gacceptor_gain0.9900

AlphaMissense

5007 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:99287992:A:CS84R1.000
1:99287994:C:AS84R1.000
1:99287994:C:GS84R1.000
1:99299127:T:CC211R1.000
1:99299129:C:GC211W1.000
1:99287972:T:AI77K0.999
1:99288049:T:AC103S0.999
1:99288049:T:CC103R0.999
1:99288050:G:AC103Y0.999
1:99288050:G:CC103S0.999
1:99288051:C:GC103W0.999
1:99288121:A:CS127R0.999
1:99288123:C:AS127R0.999
1:99288123:C:GS127R0.999
1:99296861:T:CF178L0.999
1:99296863:C:AF178L0.999
1:99296863:C:GF178L0.999
1:99296867:G:CG180R0.999
1:99299050:G:AG185E0.999
1:99299127:T:AC211S0.999
1:99299128:G:AC211Y0.999
1:99299128:G:CC211S0.999
1:99299128:G:TC211F0.999
1:99299193:T:AC233S0.999
1:99299193:T:CC233R0.999
1:99299194:G:AC233Y0.999
1:99299194:G:CC233S0.999
1:99299195:C:GC233W0.999
1:99301862:G:CG311R0.999
1:99301863:G:AG311D0.999

dbSNP variants (sampled 300 via entrez): RS1000103229 (1:99303528 A>G), RS1000172515 (1:99276003 A>T), RS1000181470 (1:99280677 G>A,T), RS1000189052 (1:99286323 T>C), RS1000203556 (1:99276270 G>A,C), RS1000233540 (1:99274658 C>G), RS1000327365 (1:99280164 T>C), RS1000357760 (1:99269935 A>C), RS1000485831 (1:99262956 C>A,T), RS1000539066 (1:99277641 A>C), RS1000610512 (1:99298781 G>A,T), RS1000644348 (1:99286150 A>G), RS1000760631 (1:99271686 T>C), RS1000833060 (1:99270126 A>C), RS1000892240 (1:99265932 G>A)

Disease associations

OMIM: gene MIM:607813 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

StudyTraitp-value
GCST001766_3Non-alcoholic fatty liver disease histology (other)5.000000e-06
GCST003802_1Response to citalopram or escitalopram in depression1.000000e-07
GCST006465_10Endometrial cancer (endometrioid histology)4.000000e-07
GCST009733_73Urinary metabolite levels in chronic kidney disease2.000000e-12
GCST009735_26Urinary metabolite modules (eigenmetabolites) in chronic kidney disease3.000000e-11

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0005116urinary metabolite measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, decreases methylation, increases expression3
Valproic Acidincreases expression, decreases methylation3
trichostatin Adecreases expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
geldanamycinincreases expression1
methylmercuric chloridedecreases expression1
bisphenol Aincreases expression1
ferrous chloridedecreases expression1
triadimefondecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
incobotulinumtoxinAincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation, increases methylation1
Cadmiumdecreases expression, increases abundance1
Diethylhexyl Phthalatedecreases expression1
Doxorubicindecreases expression1
Leadaffects expression1
Mercuryincreases expression1
Methotrexatedecreases expression1
Tretinoindecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Permethrindecreases expression1
Particulate Matterincreases abundance, decreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.