PLA2G7
protein-codingphospholipase A2 group VII, the group of Phospholipases
Gene summary
The protein encoded by this gene is a secreted enzyme that catalyzes the degradation of platelet-activating factor to biologically inactive products. Defects in this gene are a cause of platelet-activating factor acetylhydrolase deficiency. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013663
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Pulmonary
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PLA2G7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005084.4. 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 | 9 | 9 | ||||
| missense | 76 | 9 | 2 | 87 | ||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 3 | 3 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 2 | 5 | |||
| Total | 0 | 3 | 84 | 18 | 2 | 107 |
Highest pathogenic variant AF is 0.000058925027
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005075.3 | 11 | MANE Select | |
| Ensembl | ENSP00000274793.7 | 11 | MANE Select | |
| RefSeq | NP_001161829.1 | 11 | Standard | |
| Ensembl | ENSP00000445666.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ether lipid metabolism - Homo sapiens (human)
- IL1 and megakaryocytes in obesity
- Peptide hormone metabolism
- Synthesis, secretion, and deacylation of Ghrelin
- Metabolism of proteins
Biological Process
- lipid catabolic process
- low-density lipoprotein particle remodeling
- lipid oxidation
- plasma lipoprotein particle oxidation
- platelet activating factor metabolic process
Molecular Function
- 1-alkyl-2-acetylglycerophosphocholine esterase activity
- phospholipid binding
- hydrolase activity, acting on ester bonds
- calcium-independent phospholipase A2 activity
Cellular Component
- extracellular region
- cytoplasm
- low-density lipoprotein particle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000274793
- Coding exons
- 11
- Length
- 31493
- Individuals with no LoFs
- 125330
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 410
- Defined
- 125743
- p
- 0.00164
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.05 | 274 | 229 | 1.20 | 0.0000108 | 2919 |
| Missense (PolyPhen) | 108 | 87.815 | 1.2299 | 1148 | ||
| Synonymous | -0.141 | 78 | 76.4 | 1.02 | 0.00000359 | 805 |
| Loss of Function | -1.17 | 29 | 23.0 | 1.26 | 0.00000107 | 280 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.0014 | 0.0014 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00083 | 0.00083 | rare |
| South Asian | 0.0080 | 0.0079 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Modulates the action of platelet-activating factor (PAF) by hydrolyzing the sn-2 ester bond to yield the biologically inactive lyso-PAF. Has a specificity for substrates with a short residue at the sn-2 position. It is inactive against long-chain phospholipids.;
- Disease
- DISEASE: Asthma (ASTHMA) [MIM:600807]: The most common chronic disease affecting children and young adults. It is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. It is characterized by recurrent attacks of paroxysmal dyspnea, with wheezing due to spasmodic contraction of the bronchi. {ECO:0000269|PubMed:10733466}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Atopic hypersensitivity (ATOPY) [MIM:147050]: A condition characterized by predisposition to develop hypersensitivity reactions. Atopic individuals can develop eczema, allergic rhinitis and allergic asthma. {ECO:0000269|PubMed:10733466}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.304
Intolerance Scores
- LoFtool
- 1.00
- RVIS EVS
- 0.58
- RVIS percentile EVS
- 82.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0145
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |