PLA2G4E
protein-codingphospholipase A2 group IVE, the group of C2 domain containing phospholipases|Phospholipases
Gene summary
This gene encodes a member of the cytosolic phospholipase A2 group IV family. Members of this family are involved in regulation of membrane tubule-mediated transport. The enzyme encoded by this member of the family plays a role in trafficking through the clathrin-independent endocytic pathway. The enzyme regulates the recycling process via formation of tubules that transport internalized clathrin-independent cargo proteins back to the cell surface. [provided by RefSeq, Jan 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~69.8 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 PLA2G4E variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001395548.1. 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 | 123 | 4 | 4 | 131 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 123 | 4 | 6 | 133 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001382477.1 | 20 | MANE Select | |
| Ensembl | ENSP00000512406.1 | 20 | MANE Select | |
| RefSeq | NP_001193599.1 | 20 | Standard | |
| Ensembl | ENSP00000382434.3 | 20 | 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
- phospholipid metabolic process
- phosphatidylinositol acyl-chain remodeling
- phosphatidylserine acyl-chain remodeling
- phosphatidylcholine acyl-chain remodeling
- phosphatidylethanolamine 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
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000399518
- Coding exons
- 20
- Length
- 69609
- Individuals with no LoFs
- 124946
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 94
- Defined
- 125040
- p
- 0.000376
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.14 | 412 | 483 | 0.854 | 0.0000269 | 5646 |
| Missense (PolyPhen) | 138 | 184.71 | 0.7471 | 2204 | ||
| Synonymous | -0.489 | 207 | 198 | 1.04 | 0.0000116 | 1651 |
| Loss of Function | 2.87 | 28 | 49.9 | 0.561 | 0.00000287 | 513 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00040 | 0.00038 | rare |
| Latino/Admixed American | 0.00061 | 0.00061 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00040 | 0.00038 | rare |
| Finnish | 0.00019 | 0.00019 | rare |
| European (Non-Finnish) | 0.00035 | 0.00034 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position. {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- 0.32
- RVIS percentile EVS
- 72.8
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.344
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |