PLA2G12A
protein-codingphospholipase A2 group XIIA, the group of Phospholipases
Gene summary
Secreted phospholipase A2 (sPLA2) enzymes liberate arachidonic acid from phospholipids for production of eicosanoids and exert a variety of physiologic and pathologic effects. Group XII sPLA2s, such as PLA2G12A, have relatively low specific activity and are structurally and functionally distinct from other sPLA2s (Gelb et al., 2000 [PubMed 11031251]).[supplied by OMIM, Mar 2008]
- PLA2G12
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.1 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 PLA2G12A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030821.5. 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 | 0 | |||||
| missense | 42 | 1 | 43 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 43 | 1 | 0 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_110448.2 | 4 | MANE Select | |
| Ensembl | ENSP00000243501.5 | 4 | MANE Select | |
| Ensembl | ENSP00000425274.1 | 4 | Standard | |
| Ensembl | ENSP00000425274.1 | 4 | 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
- phosphatidic acid biosynthetic process
- biological_process
- lipid catabolic process
- phosphatidylglycerol acyl-chain remodeling
- phosphatidylinositol acyl-chain remodeling
Molecular Function
- phospholipase A2 activity
- calcium ion binding
- calcium-dependent phospholipase A2 activity
- phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine)
- phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)
Cellular Component
- extracellular region
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000243501
- Coding exons
- 4
- Length
- 20089
- Individuals with no LoFs
- 125685
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 63
- Defined
- 125748
- p
- 0.000251
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.199 | 112 | 106 | 1.05 | 0.00000508 | 1226 |
| Missense (PolyPhen) | 43 | 46.851 | 0.9178 | 561 | ||
| Synonymous | 0.782 | 36 | 42.5 | 0.847 | 0.00000215 | 367 |
| Loss of Function | 0.694 | 6 | 8.14 | 0.737 | 4.28e-7 | 97 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0027 | 0.0027 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. Does not exhibit detectable activity toward sn-2-arachidonoyl- or linoleoyl- phosphatidylcholine or -phosphatidylethanolamine. {ECO:0000269|PubMed:12522102}.;
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- LoFtool
- 0.390
- RVIS EVS
- 0.22
- RVIS percentile EVS
- 67.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.229
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |