PLA2G4F
protein-codingphospholipase A2 group IVF, the group of Phospholipases|C2 domain containing phospholipases
Gene summary
Predicted to enable calcium ion binding activity; calcium-dependent phospholipid binding activity; and obsolete calcium-dependent phospholipase A2 activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within arachidonate secretion; cellular response to antibiotic; and prostaglandin biosynthetic process. Predicted to be located in mitochondrion and plasma membrane. Predicted to be active in cytosol; ruffle membrane; and vesicle. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.6 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 PLA2G4F variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_213600.4. 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 | 2 | 3 | 5 | |||
| missense | 178 | 3 | 181 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 186 | 6 | 0 | 192 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_998765.3 | 20 | MANE Select | |
| Ensembl | ENSP00000380442.4 | 20 | MANE Select | |
| Ensembl | ENSP00000290497.7 | 2 | Standard | |
| Ensembl | ENSP00000456697.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
- Platelet activation - Homo sapiens (human)
- Oxytocin signaling pathway - Homo sapiens (human)
- Fc epsilon RI signaling pathway - Homo sapiens (human)
- Fc gamma R-mediated phagocytosis - Homo sapiens (human)
Biological Process
- prostaglandin biosynthetic process
- phospholipid metabolic process
- phosphatidylglycerol acyl-chain remodeling
- phosphatidylinositol acyl-chain remodeling
- phosphatidylserine acyl-chain remodeling
Molecular Function
- lysophospholipase activity
- phospholipase A2 activity
- calcium ion binding
- calcium-dependent phospholipid binding
- phospholipase A1 activity
Cellular Component
- cytoplasm
- lysosomal membrane
- cytosol
- vesicle
- ruffle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000382396
- Coding exons
- 20
- Length
- 15508
- Individuals with no LoFs
- 125524
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 223
- Defined
- 125748
- p
- 0.000891
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.532 | 530 | 497 | 1.07 | 0.0000292 | 5436 |
| Missense (PolyPhen) | 129 | 130.33 | 0.98979 | 1574 | ||
| Synonymous | -0.148 | 212 | 209 | 1.01 | 0.0000127 | 1737 |
| Loss of Function | 0.597 | 44 | 48.5 | 0.908 | 0.00000261 | 490 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00075 | 0.00074 | rare |
| Latino/Admixed American | 0.00087 | 0.00087 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0.00024 | 0.00023 | rare |
| European (Non-Finnish) | 0.00085 | 0.00084 | rare |
| South Asian | 0.0022 | 0.0021 | notable |
| Other | 0.00099 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position. Has higher enzyme activity for phosphatidylethanolamine than phosphatidylcholine (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0982
Intolerance Scores
- LoFtool
- 0.813
- RVIS EVS
- 1.33
- RVIS percentile EVS
- 94.1
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0990
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |