PLAAT3

gene
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Also known as HREV107H-REV107-1HREV107-3MGC118754.AdPLAPLAAT-3

Summary

PLAAT3 (phospholipase A and acyltransferase 3, HGNC:17825) is a protein-coding gene on chromosome 11q12.3-q13.1, encoding Phospholipase A and acyltransferase 3 (P53816). Exhibits both phospholipase A1/2 and acyltransferase activities.

Enables N-acyltransferase activity; lipid binding activity; and phospholipase activity. Involved in N-acylphosphatidylethanolamine metabolic process. Predicted to be located in several cellular components, including lysosome; nuclear envelope; and peroxisome. Predicted to be active in cytoplasm. Biomarker of seminoma.

Source: NCBI Gene 11145 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): lipodystrophy, familial partial, type 9 (Strong, GenCC)
  • Clinical variants (ClinVar): 51 total — 3 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 49
  • Druggable target: yes
  • MANE Select transcript: NM_001128203

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17825
Approved symbolPLAAT3
Namephospholipase A and acyltransferase 3
Location11q12.3-q13.1
Locus typegene with protein product
StatusApproved
AliasesHREV107, H-REV107-1, HREV107-3, MGC118754., AdPLA, PLAAT-3
Ensembl geneENSG00000176485
Ensembl biotypeprotein_coding
OMIM613867
Entrez11145

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 14 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000323646, ENST00000394613, ENST00000415826, ENST00000540943, ENST00000544269, ENST00000873643, ENST00000873644, ENST00000873645, ENST00000873646, ENST00000873647, ENST00000873648, ENST00000911543, ENST00000911544, ENST00000911545, ENST00000911546, ENST00000911547

RefSeq mRNA: 2 — MANE Select: NM_001128203 NM_001128203, NM_007069

CCDS: CCDS8047

Canonical transcript exons

ENST00000415826 — 5 exons

ExonStartEnd
ENSE000016715516361438563614433
ENSE000017120766361400063614068
ENSE000035755486359806163598163
ENSE000036019926359010063590368
ENSE000039096226357446263575046

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 99.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.9610 / max 709.3708, expressed in 1545 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter IDTPM avgSamples expressed
12031811.06311457
1203178.65881035
1203191.8765941
1203121.4697621
1203130.9424381
1203140.7158258
1203110.6362253
1203160.4155252
1203090.2824123
1203100.270761

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
C1 segment of cervical spinal cordUBERON:000646999.33gold quality
spinal cordUBERON:000224099.01gold quality
corpus callosumUBERON:000233698.76gold quality
adipose tissueUBERON:000101398.51gold quality
adipose tissue of abdominal regionUBERON:000780898.47gold quality
tibial nerveUBERON:000132398.44gold quality
inferior vagus X ganglionUBERON:000536398.43gold quality
omental fat padUBERON:001041498.43gold quality
left testisUBERON:000453398.41gold quality
peritoneumUBERON:000235898.40gold quality
right testisUBERON:000453498.32gold quality
subcutaneous adipose tissueUBERON:000219098.21gold quality
lateral globus pallidusUBERON:000247698.16gold quality
middle frontal gyrusUBERON:000270298.10gold quality
substantia nigra pars reticulataUBERON:000196697.93gold quality
apex of heartUBERON:000209897.79gold quality
putamenUBERON:000187497.59gold quality
globus pallidusUBERON:000187597.59gold quality
substantia nigraUBERON:000203897.59gold quality
connective tissueUBERON:000238497.53gold quality
midbrainUBERON:000189197.49gold quality
inferior olivary complexUBERON:000212797.47gold quality
subthalamic nucleusUBERON:000190697.46gold quality
amygdalaUBERON:000187697.40gold quality
medial globus pallidusUBERON:000247797.39gold quality
heart left ventricleUBERON:000208497.29gold quality
hypothalamusUBERON:000189897.23gold quality
cardiac ventricleUBERON:000208297.21gold quality
right atrium auricular regionUBERON:000663197.13gold quality
hindlimb stylopod muscleUBERON:000425297.12gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 10.

ExperimentMarker?Max mean expression
E-MTAB-11121yes709.62
E-GEOD-134144yes34.64
E-MTAB-10287yes30.25
E-MTAB-8410yes21.90
E-MTAB-6701yes18.15
E-HCAD-1yes15.60
E-GEOD-84465yes12.13
E-MTAB-9388yes11.46
E-MTAB-6678yes9.17
E-MTAB-6524no286.05
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ETS2, FOXC1, IRF1, PPARG, SP1, SP3, TP53

miRNA regulators (miRDB)

18 targeting PLAAT3, 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-340-5P100.0072.504437
HSA-MIR-548P99.9872.253784
HSA-MIR-130599.9171.433443
HSA-MIR-345-3P99.8970.231421
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-670-5P99.6769.941565
HSA-MIR-4743-3P99.6268.122095
HSA-MIR-317199.4969.06776
HSA-MIR-4652-3P99.3370.022742
HSA-MIR-223-5P99.2468.821206
HSA-MIR-26B-3P98.7167.491102
HSA-MIR-6830-3P98.6268.071760
HSA-MIR-58198.3967.42835
HSA-MIR-4778-5P97.9668.061634
HSA-MIR-6787-3P97.7566.171233
HSA-MIR-6859-3P97.2664.69428
HSA-MIR-1251-5P95.7864.10374
HSA-MIR-4655-3P82.4362.9260

Literature-anchored findings (GeneRIF, showing 20)

  • Contact inhibition of growth and growth arrest caused by histone deacetylase inhibitors probably use the same mechanism to stimulate H-rev107 expression via histone acetylation in NIH3T3 cells (PMID:12054741)
  • H-REV107-1 is deficient in its function as a tumor suppressor in non-small cell lung carcinomas. (PMID:17003497)
  • Identification and functional characterization of adipose-specific phospholipase A2 (AdPLA) (PMID:18614531)
  • AdPLA ablation increases lipolysis and prevents obesity induced by high-fat feeding or leptin deficiency. (PMID:19136964)
  • role of PKC isoenzymes in PP2A and HRSL3(H-REV107-1) tumor suppressor-dependent cell death induction in ovarian carcinoma cell line; verified contribution to PP2A- and HRLS3-dependent apoptosis for PKCzeta suggesting a proapoptotic function of this kinase (PMID:20501645)
  • Data show that acyl-modified forms of HRAS-like tumor suppressors HRASLS2 and HRASLS3 mimicking lipolytic activity of lecithin retinol acyltransferase LRAT. (PMID:22605381)
  • an alternate mechanism for AdPLA in promoting adipose tissue lipolysis that is not contingent on the release of arachidonic acid and that is compatible with its combined PLA(1)/A(2) activity (PMID:22923616)
  • Our study further suggests that the PLA/AT activity of H-rev107 may play an important role in H-rev107-mediated RAS suppression. (PMID:24884338)
  • several mutant p53 proteins bind the Pla2g16 promoter at E26 transformation-specific (ETS) binding motifs and knockdown of ETS2 suppressed mutant p53 induction of Pla2g16. (PMID:25024203)
  • crystal structure of the HRASLS3-LRAT chimeric enzyme in a thioester catalytic intermediate state revealed a major structural rearrangement accompanied by three-dimensional domain swapping dimerization not observed in native HRASLS (PMID:25383759)
  • the flexible main loop of H-REV107, but not that of TIG3, is critical for its NTD to modulate its CTD in inducing cell death. (PMID:25871522)
  • Results show that osteosarcoma patients with metastasis showed higher expression of PLA2G16 at both the mRNA and protein levels and shorter overall survival suggesting it as significant prognostic factor for poor outcome. (PMID:25993412)
  • suggest a novel regulatory mechanism for peroxisome biogenesis through the interaction between Pex19p and PLA/AT-3 (PMID:26018079)
  • our results revealed that H-rev107 is also involved in lipid accumulation in liver cells through the POR pathway via its PLA2 activity. (PMID:26381418)
  • Demonstrate increased PLA2G16 expression activates the MAPK pathway to enhance osteosarcoma metastasis. (PMID:26933804)
  • study uncovers two competing processes triggered by Picornaviridae virus entry: activation of a pore-activated clearance pathway and recruitment of a PLA2G16 phospholipase to enable genome release (PMID:28077878)
  • PLA2G16 SNPs are associated with the colorectal cancer risk in the Chinese population. (PMID:30343388)
  • PLA2G16 methylation defines an extensive field defect in histologically normal prostate tissue associated with PC. (PMID:31233548)
  • Skeletal muscle expression of adipose-specific phospholipase in peripheral artery disease. (PMID:32853041)
  • PLA2G16 is a mutant p53/KLF5 transcriptional target and promotes glycolysis of pancreatic cancer. (PMID:32985124)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriolratb.2ENSDARG00000077652
mus_musculusPlaat3ENSMUSG00000060675
rattus_norvegicusPlaat3ENSRNOG00000021206

Paralogs (7): LRAT (ENSG00000121207), PLAAT1 (ENSG00000127252), PLAAT4 (ENSG00000133321), PLAAT2 (ENSG00000133328), LRATD1 (ENSG00000162981), PLAAT5 (ENSG00000168004), LRATD2 (ENSG00000168672)

Protein

Protein identifiers

Phospholipase A and acyltransferase 3P53816 (reviewed: P53816)

Alternative names: Adipose-specific phospholipase A2, Group XVI phospholipase A1/A2, H-rev 107 protein homolog, HRAS-like suppressor 1, HRAS-like suppressor 3, HREV107-3, Renal carcinoma antigen NY-REN-65

All UniProt accessions (2): P53816, F5H7E5

UniProt curated annotations — full annotation on UniProt →

Function. Exhibits both phospholipase A1/2 and acyltransferase activities. Shows phospholipase A1 (PLA1) and A2 (PLA2) activity, catalyzing the calcium-independent release of fatty acids from the sn-1 or sn-2 position of glycerophospholipids. For most substrates, PLA1 activity is much higher than PLA2 activity. Shows O-acyltransferase activity,catalyzing the transfer of a fatty acyl group from glycerophospholipid to the hydroxyl group of lysophospholipid. Shows N-acyltransferase activity, catalyzing the calcium-independent transfer of a fatty acyl group at the sn-1 position of phosphatidylcholine (PC) and other glycerophospholipids to the primary amine of phosphatidylethanolamine (PE), forming N-acylphosphatidylethanolamine (NAPE), which serves as precursor for N-acylethanolamines (NAEs). Exhibits high N-acyltransferase activity and low phospholipase A1/2 activity. Required for complete organelle rupture and degradation that occur during eye lens terminal differentiation, when fiber cells that compose the lens degrade all membrane-bound organelles in order to provide lens with transparency to allow the passage of light. Organelle membrane degradation is probably catalyzed by the phospholipase activity. (Microbial infection) Acts as a host factor for picornaviruses: required during early infection to promote viral genome release into the cytoplasm. May act as a cellular sensor of membrane damage at sites of virus entry, which relocalizes to sites of membrane rupture upon virus unfection. Facilitates safe passage of the RNA away from LGALS8, enabling viral genome translation by host ribosome. May also be involved in initiating pore formation, increasing pore size or in maintaining pores for genome delivery. The lipid-modifying enzyme activity is required for this process.

Subunit / interactions. Interacts with PPP2R1A; this interaction might decrease PP2A activity.

Subcellular location. Cell membrane. Cytoplasm. Cytosol. Perinuclear region. Peroxisome membrane. Mitochondrion membrane. Nucleus envelope. Lysosome membrane. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed. Low expression, if any, in hematopoietic cells and thymus. In testis, confined to round spermatids. Expressed in normal ovarian epithelial cells. Down-regulated in some ovarian carcinomas and testicular germ cell tumors. Highly expressed in white adipose tissue.

Disease relevance. Lipodystrophy, familial partial, 9 (FPLD9) [MIM:620683] An autosomal recessive form of partial lipodystrophy, a disorder characterized by abnormal subcutaneous fat distribution. FPLD9 patients are lean and show muscular hypertrophy, insulin-resistant diabetes with hyperinsulinemia, hypertriglyceridemia with low high-density lipoprotein (HDL) cholesterol, liver steatosis, and polycystic ovary syndrome with hirsutism. Some patients have more generalized lipoatrophy, whereas others have abnormal fat accumulation in the face and neck regions and show cushingoid or acromegalic facial features. Most patients also have neurologic features, including demyelinating polyneuropathy, developmental delay and intellectual disability. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The C-terminal transmembrane domain is required for the targeting of the protein to damaged organelles.

Induction. By IFNG and IRF1.

Similarity. Belongs to the H-rev107 family.

RefSeq proteins (2): NP_001121675, NP_009000 (=MANE)

Domains & families (InterPro)

IDNameType
IPR007053LRAT_domDomain
IPR051496H-rev107_PLA/ATFamily

Pfam: PF04970

Catalyzed reactions (Rhea), 12 shown:

  • a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) (RHEA:15801)
  • a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 2-acyl-sn-glycero-3-phosphocholine + a fatty acid + H(+) (RHEA:18689)
  • 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphocholine + (9Z)-octadecenoate + H(+) (RHEA:38779)
  • 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + H2O = 2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + hexadecanoate + H(+) (RHEA:38783)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphocholine + (5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) (RHEA:40427)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoethanolamine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphoethanolamine + (5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) (RHEA:40431)
  • 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine + H2O = 2-hexadecanoyl-sn-glycero-3-phosphocholine + hexadecanoate + H(+) (RHEA:40487)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine + H2O = 2-(5Z,8Z,11Z,14Z)-eicosatetraenoyl-sn-glycero-3-phosphocholine + hexadecanoate + H(+) (RHEA:40571)
  • 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine + H2O = (9Z,12Z)-octadecadienoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine + H(+) (RHEA:40811)
  • 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphoethanolamine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphoethanolamine + (9Z,12Z)-octadecadienoate + H(+) (RHEA:40815)
  • 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + H2O = 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + (9Z)-octadecenoate + H(+) (RHEA:40923)
  • 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine + H2O = 2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine + hexadecanoate + H(+) (RHEA:40971)

UniProt features (27 total): strand 8, helix 4, mutagenesis site 3, active site 3, topological domain 2, turn 2, chain 1, sequence conflict 1, transmembrane region 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
7ZOMX-RAY DIFFRACTION1.6
7C3ZX-RAY DIFFRACTION1.96
4DOTX-RAY DIFFRACTION1.96
4Q95X-RAY DIFFRACTION2.2
7C41X-RAY DIFFRACTION2.28
4FA0X-RAY DIFFRACTION2.65
2KYTSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P53816-F177.120.56

Functional residue map

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

Catalytic / active sites (3): 23; 35; 113 (acyl-thioester intermediate)

Mutagenesis-validated functional residues (3):

PositionPhenotype
39–57induces a major structural rearrangement accompanied by domain-swapping dimerization and changes in substrate-specificit
113no effect on ppp2r1a-binding. impaired ability to act as a host factor for picornaviruses.
23no effect on ppp2r1a-binding.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-1482788Acyl chain remodelling of PC
R-HSA-1482801Acyl chain remodelling of PS
R-HSA-1482839Acyl chain remodelling of PE
R-HSA-1482922Acyl chain remodelling of PI

MSigDB gene sets: 451 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_LENS_FIBER_CELL_DIFFERENTIATION, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, GOCC_VACUOLAR_MEMBRANE, GOBP_MEMBRANE_DISASSEMBLY, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, chr11q13

GO Biological Process (14): triglyceride metabolic process (GO:0006641), phospholipid metabolic process (GO:0006644), peroxisome organization (GO:0007031), phospholipid biosynthetic process (GO:0008654), response to bacterium (GO:0009617), lipid catabolic process (GO:0016042), membrane disassembly (GO:0030397), phosphatidylethanolamine acyl-chain remodeling (GO:0036152), ether lipid metabolic process (GO:0046485), N-acylphosphatidylethanolamine metabolic process (GO:0070292), lens fiber cell differentiation (GO:0070306), organelle disassembly (GO:1903008), regulation of adipose tissue development (GO:1904177), lipid metabolic process (GO:0006629)

GO Molecular Function (9): A2-type glycerophospholipase activity (GO:0004623), lipid binding (GO:0008289), glycerophospholipid phospholipase A1 activity (GO:0008970), obsolete N-acyltransferase activity (GO:0016410), acyltransferase activity (GO:0016746), glycerophospholipase activity (GO:0004620), protein binding (GO:0005515), transferase activity (GO:0016740), hydrolase activity (GO:0016787)

GO Cellular Component (15): nuclear envelope (GO:0005635), cytoplasm (GO:0005737), mitochondrion (GO:0005739), lysosome (GO:0005764), lysosomal membrane (GO:0005765), peroxisome (GO:0005777), peroxisomal membrane (GO:0005778), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), cytosol (GO:0005829), plasma membrane (GO:0005886), mitochondrial membrane (GO:0031966), perinuclear region of cytoplasm (GO:0048471), nucleus (GO:0005634), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Glycerophospholipid biosynthesis4

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cytoplasm4
lipid metabolic process3
intracellular membrane-bounded organelle3
organelle organization2
cellular component disassembly2
binding2
catalytic activity2
endomembrane system2
organelle membrane2
acylglycerol metabolic process1
organophosphate metabolic process1
phospholipid metabolic process1
lipid biosynthetic process1
organophosphate biosynthetic process1
response to other organism1
catabolic process1
membrane organization1
phosphatidylcholine metabolic process1
phosphatidylethanolamine metabolic process1
lens development in camera-type eye1
epithelial cell differentiation1
regulation of developmental process1
adipose tissue development1
primary metabolic process1
glycerophospholipase activity1
carboxylic ester hydrolase activity1
A1-type glycerophospholipase activity1
transferase activity1
phospholipase activity1
nucleus1
organelle envelope1
intracellular anatomical structure1
lytic vacuole1
lysosome1
lytic vacuole membrane1
microbody1
peroxisome1
microbody membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1

Protein interactions and networks

STRING

2908 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PLAAT3CRABP2P29373747
PLAAT3RARGP13631642
PLAAT3PLA2G15Q8NCC3640
PLAAT3PLA2G2AP14555582
PLAAT3SETD3Q86TU7563
PLAAT3RARBP10826553
PLAAT3PEX19P40855543
PLAAT3PLA2G4AP47712528
PLAAT3PLA2G3Q9NZ20499
PLAAT3PLA2G2DQ9UNK4496
PLAAT3PLA2G10O15496490
PLAAT3PLA2G6O60733488
PLAAT3KRASP01116485
PLAAT3PLA2G5P39877483
PLAAT3ENPP2Q13822472

IntAct

26 interactions, top by confidence:

ABTypeScore
UBQLN1PLAAT3psi-mi:“MI:0915”(physical association)0.780
PLAAT3UBQLN1psi-mi:“MI:0915”(physical association)0.780
PPP2R1APLAAT3psi-mi:“MI:0915”(physical association)0.640
PLAAT3PPP2R1Apsi-mi:“MI:0915”(physical association)0.640
PLAAT3PPP2R1Apsi-mi:“MI:0403”(colocalization)0.640
PLAAT3UBQLN1psi-mi:“MI:0915”(physical association)0.560
UBQLN1PLAAT3psi-mi:“MI:0915”(physical association)0.560
PLAAT3UBQLN2psi-mi:“MI:0915”(physical association)0.560
PLAAT3OCLNpsi-mi:“MI:0914”(association)0.350
PRKCSHKLRG2psi-mi:“MI:0914”(association)0.350
MFSD14AFAM171A2psi-mi:“MI:0914”(association)0.350
PLAAT3UBQLN2psi-mi:“MI:0915”(physical association)0.000
PLAAT3UBQLN1psi-mi:“MI:0915”(physical association)0.000
NRIP1PLAAT3psi-mi:“MI:0915”(physical association)0.000
PLAAT3UBQLN4psi-mi:“MI:0915”(physical association)0.000

BioGRID (19): UBQLN1 (Two-hybrid), UBQLN1 (Two-hybrid), HRAS (Affinity Capture-Western), PLA2G16 (Affinity Capture-Western), PLA2G16 (Affinity Capture-MS), PLA2G16 (Two-hybrid), UBQLN2 (Two-hybrid), OCLN (Affinity Capture-MS), MIB2 (Affinity Capture-MS), PLA2G16 (Affinity Capture-MS), PLA2G16 (Two-hybrid), PLA2G16 (Affinity Capture-MS), PLA2G16 (Affinity Capture-MS), PLA2G16 (Affinity Capture-RNA), PLA2G16 (Two-hybrid)

ESM2 similar proteins: A0A0R4IY06, B8BKI7, D2KX21, D3ZLY0, E0CSI1, O54909, O75452, O88451, P00860, P09057, P11926, P14019, P17516, P27117, P27118, P27119, P27120, P50170, P53816, P53817, P55006, P70694, P97872, Q04799, Q1XAA8, Q2R483, Q3T067, Q3UFY7, Q571F8, Q5R611, Q6AY30, Q6AYP7, Q6P4H8, Q86TW2, Q86V88, Q8R127, Q8R2J9, Q8R3U1, Q8VDG3, Q93V51

Diamond homologs: A0A0R4IY06, D2KX21, P53816, P53817, Q4KLN5, Q5R611, Q8R3U1, Q96KN8, Q9BGL2, Q9CPX5, Q9HDD0, Q9JI61, Q9NWW9, Q9QZU4, Q9UL19, O95237, Q9JI60, Q3ZCA1, Q96KN1, Q96KN4, Q9D650

SIGNOR signaling

2 interactions.

AEffectBMechanism
PLAAT3down-regulatesPPP2CA
PLAAT3down-regulatesPPP2CB

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic3
Likely pathogenic1
Uncertain significance38
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
2691740NM_001128203.2(PLAAT3):c.16-4823_118+167delPathogenic
2691741NM_001128203.2(PLAAT3):c.286dup (p.Ala96fs)Pathogenic
2691742NM_001128203.2(PLAAT3):c.339C>A (p.Cys113Ter)Pathogenic
4845839NM_001128203.2(PLAAT3):c.387+2T>CLikely pathogenic

SpliceAI

655 predictions. Top by Δscore:

VariantEffectΔscore
11:63575044:GACCT:Gacceptor_loss1.0000
11:63575046:CCT:Cacceptor_loss1.0000
11:63575047:CT:Cacceptor_loss1.0000
11:63575048:T:Aacceptor_loss1.0000
11:63590095:CGCA:Cdonor_loss1.0000
11:63590096:GCACC:Gdonor_loss1.0000
11:63590097:CAC:Cdonor_loss1.0000
11:63590378:C:CTacceptor_gain1.0000
11:63598059:A:ACdonor_gain1.0000
11:63598060:C:CCdonor_gain1.0000
11:63613998:A:ACdonor_gain1.0000
11:63613999:C:CCdonor_gain1.0000
11:63614018:C:Adonor_gain1.0000
11:63574901:C:CAdonor_gain0.9900
11:63590157:A:ACdonor_gain0.9900
11:63590158:C:CCdonor_gain0.9900
11:63590364:CTCAC:Cacceptor_gain0.9900
11:63590365:TCAC:Tacceptor_gain0.9900
11:63590366:CAC:Cacceptor_gain0.9900
11:63590366:CACC:Cacceptor_gain0.9900
11:63590369:C:CAacceptor_loss0.9900
11:63590369:C:CCacceptor_gain0.9900
11:63590370:T:Cacceptor_loss0.9900
11:63590378:C:Tacceptor_gain0.9900
11:63597628:AGATC:Adonor_gain0.9900
11:63598160:CTGG:Cacceptor_gain0.9900
11:63598164:C:CCacceptor_gain0.9900
11:63613999:CA:Cdonor_gain0.9900
11:63613999:CAA:Cdonor_gain0.9900
11:63613999:CAAT:Cdonor_gain0.9900

AlphaMissense

1058 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:63590126:G:TR121S0.994
11:63590151:G:CN112K0.991
11:63590151:G:TN112K0.991
11:63598107:C:AW24C0.991
11:63598107:C:GW24C0.991
11:63598109:A:GW24R0.991
11:63598109:A:TW24R0.991
11:63590139:A:CF116L0.990
11:63590139:A:TF116L0.990
11:63590141:A:GF116L0.990
11:63598141:A:GL13P0.990
11:63590106:A:CS127R0.989
11:63590106:A:TS127R0.989
11:63590108:T:GS127R0.989
11:63590128:A:GL120P0.989
11:63598078:A:TV34D0.989
11:63590149:C:TC113Y0.988
11:63590308:A:TV60E0.987
11:63590125:C:GR121P0.986
11:63590140:A:GF116S0.985
11:63590146:T:AE114V0.985
11:63590150:A:GC113R0.985
11:63598106:C:GA25P0.985
11:63590145:C:AE114D0.984
11:63590145:C:GE114D0.984
11:63590148:G:CC113W0.984
11:63598074:A:CH35Q0.984
11:63598074:A:TH35Q0.984
11:63590126:G:CR121G0.983
11:63598081:A:TV33E0.982

dbSNP variants (sampled 300 via entrez): RS1000036247 (11:63614172 CG>C), RS1000073148 (11:63604260 T>A), RS1000227954 (11:63587678 A>C), RS1000357723 (11:63600804 A>G), RS1000429992 (11:63613913 G>C), RS1000450898 (11:63593125 G>T), RS1000474695 (11:63606153 A>C), RS1000618823 (11:63594676 G>A,C), RS1000813685 (11:63601131 T>C), RS1000816281 (11:63594556 T>C), RS1000845492 (11:63575813 T>TA), RS1000911442 (11:63582372 G>A), RS1000931269 (11:63582578 C>T), RS1000932068 (11:63618759 A>G), RS1001106721 (11:63582639 A>G)

Disease associations

OMIM: gene MIM:613867 | disease phenotypes: MIM:620683

GenCC curated gene-disease

DiseaseClassificationInheritance
lipodystrophy, familial partial, type 9StrongAutosomal recessive

Mondo (1): lipodystrophy, familial partial, type 9 (MONDO:0958034)

Orphanet (1): Lipodystrophy-demyelinating peripheral sensory-motor neuropathy syndrome (Orphanet:686999)

HPO phenotypes

49 total (30 of 49 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000147Polycystic ovaries
HP:0000303Mandibular prognathia
HP:0000369Low-set ears
HP:0000444Convex nasal ridge
HP:0000448Prominent nose
HP:0000470Short neck
HP:0000490Deeply set eye
HP:0000771Gynecomastia
HP:0000821Hypothyroidism
HP:0000822Hypertension
HP:0000826Precocious puberty
HP:0000831Insulin-resistant diabetes mellitus
HP:0000842Hyperinsulinemia
HP:0000956Acanthosis nigricans
HP:0001007Hirsutism
HP:0001249Intellectual disability
HP:0001263Global developmental delay
HP:0001284Areflexia
HP:0001397Hepatic steatosis
HP:0001761Pes cavus
HP:0001771Achilles tendon contracture
HP:0002064Spastic gait
HP:0002076Migraine
HP:0002155Hypertriglyceridemia
HP:0002240Hepatomegaly
HP:0002650Scoliosis
HP:0002808Kyphosis
HP:0002829Arthralgia
HP:0002857Genu valgum

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3831244 (SINGLE PROTEIN)

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

ChEMBL bioactivities

33 potent at pChembl≥5 of 33 total, top 33 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.00IC50100nMCHEMBL4633449
7.00IC50100nMCHEMBL4639199
6.90IC50125.9nMCHEMBL4639242
6.80IC50158.5nMCHEMBL4639478
6.80IC50158.5nMCHEMBL4649677
6.70IC50199.5nMCHEMBL4641977
6.60IC50251.2nMCHEMBL4643099
6.60IC50251.2nMCHEMBL4643782
6.60IC50251.2nMCHEMBL4644464
6.60IC50251.2nMCHEMBL4636806
6.40IC50398.1nMCHEMBL4645342
6.10IC50794.3nMCHEMBL4636379
6.00IC501000nMCHEMBL4643675
6.00IC501000nMCHEMBL4636463
6.00IC501000nMCHEMBL4640863
6.00IC501000nMCHEMBL4643908
5.90IC501259nMCHEMBL4642795
5.80IC501585nMCHEMBL4646350
5.80IC501585nMCHEMBL4632512
5.80IC501585nMCHEMBL4634598
5.80IC501585nMCHEMBL4645578
5.70IC501995nMCHEMBL4640676
5.70IC501995nMCHEMBL4639235
5.70IC501995nMCHEMBL4644324
5.60IC502512nMCHEMBL4645552
5.60IC502512nMCHEMBL4636625
5.50IC503162nMCHEMBL4641818
5.50IC503162nMCHEMBL4636282
5.40IC503981nMCHEMBL4648272
5.30IC505012nMCHEMBL4641304
5.30IC505012nMCHEMBL4646429
5.10IC507943nMCHEMBL4638043
5.10IC507943nMCHEMBL4649884

PubChem BioAssay actives

33 with measured affinity, of 57 total; 33 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-(3,4-dichlorophenyl)-2-oxo-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.1000uM
2-oxo-5-phenyl-N-[2-[4-[[5-(trifluoromethyl)-2-pyridinyl]oxy]phenyl]ethyl]pentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.1000uM
N-[2-(4-methylphenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.1259uM
N-[2-(4-bromophenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.1585uM
2-oxo-5-phenyl-N-[2-[4-[[6-(trifluoromethyl)-3-pyridinyl]oxy]phenyl]ethyl]pentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.1585uM
N-[2-(3-chlorophenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.1995uM
N-[2-[4-(2-chloropyrimidin-4-yl)oxyphenyl]ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.2512uM
2-oxo-5-phenyl-N-[2-(4-pyrazin-2-yloxyphenyl)ethyl]pentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.2512uM
N-[2-(2,4-dichlorophenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.2512uM
2-oxo-N-[2-(4-phenoxyphenyl)ethyl]-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.2512uM
2-oxo-5-phenyl-N-(2-phenylethyl)pentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.3981uM
N-[2-(4-methoxyphenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic500.7943uM
4-(4-chlorophenyl)-2-oxo-N-(4-phenylbutyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.0000uM
2-oxo-6-phenyl-N-(2-phenylethyl)hexanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.0000uM
4-(4-chlorophenyl)-2-oxo-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.0000uM
N-[2-(3,4-dimethoxyphenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.0000uM
N-[2-(2-chlorophenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.2589uM
(E)-2-oxo-4-phenyl-N-(2-phenylethyl)but-3-enamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.5849uM
4-(3-chlorophenyl)-2-oxo-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.5849uM
N-[2-(4-hydroxyphenyl)ethyl]-2-oxo-5-phenylpentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.5849uM
N-benzyl-4-(4-chlorophenyl)-2-oxobutanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.5849uM
4-(2-chlorophenyl)-2-oxo-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.9953uM
4-(4-methylphenyl)-2-oxo-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.9953uM
2-oxo-5-phenyl-N-[2-(4-pyrimidin-2-yloxyphenyl)ethyl]pentanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic501.9953uM
(E)-4-(4-bromophenyl)-2-oxo-N-(2-phenylethyl)but-3-enamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic502.5119uM
(E)-4-(4-chlorophenyl)-2-oxo-N-(2-phenylethyl)but-3-enamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic502.5119uM
(E)-2-oxo-N-(2-phenylethyl)-4-(3-phenylphenyl)but-3-enamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic503.1623uM
4-(4-methoxyphenyl)-2-oxo-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic503.1623uM
2-oxo-4-(4-phenoxyphenyl)-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic503.9811uM
4-(4-fluorophenyl)-2-oxo-N-(2-phenylethyl)butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic505.0119uM
(E)-4-(4-methoxyphenyl)-2-oxo-N-(2-phenylethyl)but-3-enamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic505.0119uM
4-(4-chlorophenyl)-N-ethyl-2-oxobutanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic507.9433uM
2-oxo-N-(2-phenylethyl)-4-[4-(trifluoromethyl)phenyl]butanamide1666052: Inhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisic507.9433uM

CTD chemical–gene interactions

48 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression6
sodium arseniteaffects expression, decreases expression, increases expression5
Tetrachlorodibenzodioxinincreases expression3
Cadmium Chloridedecreases expression, increases abundance, increases expression3
nickel sulfateincreases expression2
entinostatincreases expression, affects cotreatment2
Benzo(a)pyrenedecreases expression, increases expression2
Cisplatinaffects expression, affects cotreatment, increases expression2
Dexamethasoneincreases expression, affects cotreatment2
Quercetinaffects cotreatment, increases expression2
Cyclosporinedecreases expression2
3,19-(2-bromobenzylidene)andrographolidedecreases response to substance, increases expression1
bisphenol Faffects cotreatment, increases expression1
dicrotophosdecreases expression1
potassium perchloratedecreases expression1
sodium arsenatedecreases expression1
arseniteaffects binding, increases reaction1
mono-(2-ethylhexyl)phthalateincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
S-(1,2-dichlorovinyl)cysteinedecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
belinostataffects cotreatment, increases expression1
ICG 001increases expression1
Grape Seed Proanthocyanidinsdecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
Temozolomideincreases expression1
Decitabineaffects expression1
Acetaminophendecreases expression1
Ascorbic Acidaffects cotreatment, increases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4626913BindingInhibition of full-length C-terminal FLAG-tagged human PLAAT3 expressed in HEK293T cell lysate preincubated for 30 mins followed by MB064 addition and measured after 20 mins by SDS-PAGE based ABPP analysisStructure-Activity Relationship Studies of α-Ketoamides as Inhibitors of the Phospholipase A and Acyltransferase Enzyme Family. — J Med Chem

Clinical trials (associated diseases)

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