PLAAT1
protein-codingphospholipase A and acyltransferase 1, the group of Phospholipase A and acyltransferase family
Gene summary
Enables acyltransferase activity, transferring groups other than amino-acyl groups and glycerophospholipase activity. Involved in N-acylphosphatidylethanolamine metabolic process and phosphatidylcholine metabolic process. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]
- HRASLS
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PLAAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020386.5. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 25 | 2 | 27 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 27 | 2 | 1 | 30 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065119.3 | 3 | MANE Select | |
| Ensembl | ENSP00000264735.4 | 3 | MANE Select | |
| RefSeq | NP_001353041.1 | 3 | Standard | |
| Ensembl | ENSP00000414431.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Glycerophospholipid biosynthesis
- Phospholipid metabolism
- Acyl chain remodelling of PE
Biological Process
- lipid catabolic process
- phosphatidylcholine metabolic process
Molecular Function
- phospholipase A2 activity
- O-acyltransferase activity
- phospholipase A1 activity
- N-acyltransferase activity
Cellular Component
- nuclear envelope lumen
- cytoplasm
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264735
- Coding exons
- 4
- Length
- 36614
- Individuals with no LoFs
- 125267
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 477
- Defined
- 125747
- p
- 0.00191
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0796 | 95 | 97.2 | 0.977 | 0.00000539 | 1734 |
| Missense (PolyPhen) | 57 | 53.616 | 1.0631 | 611 | ||
| Synonymous | 0.464 | 35 | 38.7 | 0.905 | 0.00000239 | 586 |
| Loss of Function | 0.488 | 6 | 7.44 | 0.807 | 3.98e-7 | 127 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0013 | 0.0013 | notable |
| Latino/Admixed American | 0.0014 | 0.0012 | notable |
| Ashkenazi Jewish | 0.00042 | 0.00040 | rare |
| East Asian | 0.00071 | 0.00071 | rare |
| Finnish | 0.00056 | 0.00055 | rare |
| European (Non-Finnish) | 0.0032 | 0.0031 | notable |
| South Asian | 0.00079 | 0.00069 | rare |
| Other | 0.0023 | 0.0021 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Exhibits calcium-independent phospholipase activity towards phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Also shows acyltransferase activities, transferring an acyl group of PCs to the amino group of PEs and the hydroxyl group of lyso PCs. {ECO:0000269|PubMed:21880860}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 44.89
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.186
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |