PLA2G2F
protein-codingphospholipase A2 group IIF, the group of Phospholipases
Gene summary
Enables A2-type glycerophospholipase activity. Involved in glycerophospholipid metabolic process. Predicted to be located in cytosol and extracellular region. [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 ~11.1 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 PLA2G2F variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022819.4. 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 | 2 | ||||
| missense | 45 | 4 | 49 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 46 | 6 | 0 | 52 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_073730.3 | 5 | MANE Select | |
| Ensembl | ENSP00000364243.4 | 5 | MANE Select | |
| RefSeq | NP_001347798.1 | 4 | Standard | |
| Ensembl | ENSP00000773494.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ether lipid metabolism - Homo sapiens (human)
- Glycerophospholipid metabolism - Homo sapiens (human)
- Fat digestion and absorption - Homo sapiens (human)
- Vascular smooth muscle contraction - Homo sapiens (human)
- alpha-Linolenic acid metabolism - Homo sapiens (human)
Biological Process
- phospholipid metabolic process
- phosphatidic acid biosynthetic process
- biological_process
- lipid catabolic process
- phosphatidylglycerol acyl-chain remodeling
Molecular Function
- phospholipase A2 activity
- calcium ion binding
- phospholipid binding
- calcium-dependent phospholipase A2 activity
- phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine)
Cellular Component
- extracellular region
- cytosol
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375102
- Coding exons
- 5
- Length
- 11061
- Individuals with no LoFs
- 125700
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 46
- Defined
- 125746
- p
- 0.000183
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.284 | 134 | 125 | 1.07 | 0.00000713 | 1376 |
| Missense (PolyPhen) | 47 | 45.254 | 1.0386 | 507 | ||
| Synonymous | 0.475 | 47 | 51.3 | 0.916 | 0.00000339 | 385 |
| Loss of Function | -0.304 | 8 | 7.12 | 1.12 | 3.01e-7 | 94 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000063 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0013 | 0.0012 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000064 | 0.000062 | rare |
| South Asian | 0.00032 | 0.00029 | rare |
| Other | 0.00090 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in lipid mediator production in inflammatory conditions, by providing arachidonic acid to downstream cyclooxygenases and lipoxygenases (By similarity). Phospholipase A2, which catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides (PubMed:11112443). Hydrolyzes phosphatidylethanolamine more efficiently than phosphatidylcholine, with only a modest preference for arachidonic acid versus linoelic acid at the sn-2 position. Comparable activity toward 1-palmitoyl-2-oleoyl-phosphatidylserine vesicles to that toward 1-palmitoyl-2-oleoyl-phosphatidylglycerol (By similarity). Hydrolyzes phosphatidylglycerol versus phosphatidylcholine with a 15-fold preference (PubMed:11112443). {ECO:0000250|UniProtKB:Q9QZT4, ECO:0000269|PubMed:11112443}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- LoFtool
- 0.604
- RVIS EVS
- 0.19
- RVIS percentile EVS
- 66.82
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.217
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |