GeneBe

PLAAT3

protein-coding

phospholipase A and acyltransferase 3, the group of Phospholipase A and acyltransferase family|Phospholipases

Gene summary

Enables N-acyltransferase activity; glycerophospholipase activity; and lipid binding activity. Involved in N-acylphosphatidylethanolamine metabolic process. Located in cytosol. Biomarker of seminoma. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:
  • HRASLS3
  • PLA2G16

MANE transcript

NM_001128203.2

Inheritance

AR

ClinVar variants

P:4U:43B:3

Top phenotype

Lipodystrophy, familial partial, type 9

gnomAD constraint

pLI —, LoF o/e 1.21

Max pathogenic AF

—

Genomic locus

chr11:63,573,195-63,616,883

External References & Databases

Ensembl (ENSG00000176485)NCBI Gene (11145)OMIM (613867)HGNC:17825GenCCUniProt (P53816)AlphaFoldClinVar (PLAAT3)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~43.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

lipodystrophy, familial partial, type 9LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0958034

Submitter: G2P

lipodystrophy, familial partial, type 9LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0958034

Submitter: Ambry Genetics

lipodystrophy, familial partial, type 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0958034

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Lipodystrophy, familial partial, type 9AR

Manifestation: Cardiovascular; Craniofacial; Endocrine; Musculoskeletal; Neurologic

Intervention: Cardiovascular; Endocrine

Rationale: The condition has been described as involving dyslipidemia, fatty liver, and insulin-resistant diabetes mellitus, and awareness may enable early identification and management

Refs: 37919452Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLAAT3 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 37
not providedTotal: 5
Lipodystrophy, familial partial, type 9Total: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001128203.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
3
clinvar
 7
missense
37
clinvar
 37
nonsense
1
clinvar
 1
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
clinvar
 4
Total31433050

Highest pathogenic variant AF is 0.0000065695253

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001128203.2RefSeqNP_001121675.14MANE Select
ENST00000415826.3EnsemblENSP00000389124.14MANE Select
NM_007069.3RefSeqNP_009000.24Standard
ENST00000323646.10EnsemblENSP00000320337.54Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Regulation of lipolysis in adipocytes - Homo sapiens (human)
  • Ether lipid metabolism - Homo sapiens (human)
  • Glycerophospholipid metabolism - Homo sapiens (human)
  • alpha-Linolenic acid metabolism - Homo sapiens (human)
  • Arachidonic acid metabolism - Homo sapiens (human)

Biological Process

  • triglyceride metabolic process
  • phospholipid metabolic process
  • peroxisome organization
  • phospholipid biosynthetic process
  • response to bacterium

Molecular Function

  • phospholipase A2 activity
  • protein binding
  • phospholipase A1 activity
  • transferase activity, transferring acyl groups
  • phosphatidylserine 1-acylhydrolase activity

Cellular Component

  • cellular_component
  • peroxisome
  • peroxisomal membrane
  • endoplasmic reticulum
  • cytosol

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000323646
Coding exons
4
Length
43689
Individuals with no LoFs
125728
Homozygous LoFs
0
Heterozygous LoFs
19
Defined
125747
p
0.0000756
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.178971020.9500.000006001056
Missense (PolyPhen)3028.1921.0641336
Synonymous-0.4794541.11.100.00000267315
Loss of Function-0.49086.641.212.80e-787

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.000110.00011rare
South Asian0.0000980.000098rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Lipid-modifying enzyme that acts as major regulator of adipocyte lipolysis by catalyzing the release of fatty acids from phospholipids in adipose tissue (PubMed:19615464, PubMed:19047760, PubMed:20837014, PubMed:22605381, PubMed:22923616). Shows phospholipase A1 and A2 activity, catalyzing the calcium- independent hydrolysis of acyl groups in various phosphatidylcholines (PC) and phosphatidylethanolamine (PE) (PubMed:19615464, PubMed:19047760, PubMed:20837014, PubMed:22605381, PubMed:22923616). For most substrates, phospholipase A1 activity is much higher than phospholipase A2 activity (PubMed:19047760). Phospholipase activity causes decreased intracellular levels of ether-type lipids, affecting peroxisome metabolism (By similarity). May also have acyltransferase activity: catalyzes both N-acylation of phosphatidylethanolamine to form N-acyl-phosphatidylethanolamine and O-acylation of lyso-phosphatidylcholines to form phosphatidylcholines (PubMed:22605381, PubMed:25383759). The relevance of acyltransferase activity in vivo is however unclear and would require additional evidences (PubMed:22605381, PubMed:25383759). Also has weak lysophospholipase activity (By similarity). {ECO:0000250|UniProtKB:Q8R3U1, ECO:0000269|PubMed:17374643, ECO:0000269|PubMed:19047760, ECO:0000269|PubMed:19615464, ECO:0000269|PubMed:20837014, ECO:0000269|PubMed:22605381, ECO:0000269|PubMed:22923616, ECO:0000269|PubMed:25383759}.;

Recessive Scores

pRec
0.0873

Intolerance Scores

LoFtool
0.675
RVIS EVS
-0.03
RVIS percentile EVS
51.4

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.881

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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