PLA2G2D
protein-codingphospholipase A2 group IID, the group of Phospholipases
Gene summary
This gene encodes a secreted member of the phospholipase A2 family, and is found in a cluster of related family members on chromosome 1. Phospholipase A2 family members hydrolyze the sn-2 fatty acid ester bond of glycerophospholipids to produce lysophospholipids and free fatty acid. This gene may be involved in inflammation and immune response, and in weight loss associated with chronic obstructive pulmonary disease. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.6 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 PLA2G2D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012400.4. 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 | 1 | 1 | 2 | |||
| missense | 18 | 3 | 21 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 18 | 4 | 1 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036532.1 | 4 | MANE Select | |
| Ensembl | ENSP00000364246.3 | 4 | MANE Select | |
| RefSeq | NP_001258743.1 | 3 | Standard | |
| Ensembl | ENSP00000482871.1 | 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
- CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation
- phospholipid metabolic process
- phosphatidic acid biosynthetic process
- inflammatory response
- lipid catabolic process
Molecular Function
- phospholipase A2 activity
- calcium ion binding
- phospholipid binding
- heparin binding
- heparan sulfate proteoglycan binding
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375105
- Coding exons
- 4
- Length
- 7619
- Individuals with no LoFs
- 125628
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 119
- Defined
- 125748
- p
- 0.000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.406 | 94 | 83.6 | 1.13 | 0.00000457 | 943 |
| Missense (PolyPhen) | 41 | 35.636 | 1.1505 | 399 | ||
| Synonymous | -0.964 | 40 | 33.0 | 1.21 | 0.00000170 | 264 |
| Loss of Function | -0.113 | 7 | 6.68 | 1.05 | 2.84e-7 | 75 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0037 | 0.0037 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.00085 | 0.00082 | rare |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. L-alpha-1-palmitoyl-2- linoleoyl phosphatidylethanolamine is more efficiently hydrolyzed than the other phospholipids examined.;
Recessive Scores
- pRec
- 0.0833
Intolerance Scores
- LoFtool
- 0.682
- RVIS EVS
- 1.1
- RVIS percentile EVS
- 91.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.269
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |