PLA2G10
phospholipase A2 group X, the group of Phospholipases
Basic information
Region (hg38): 16:14672548-14694308
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G10 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 2 | 0 |
Variants in PLA2G10
This is a list of pathogenic ClinVar variants found in the PLA2G10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-14672718-C-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 16-14672745-C-T | Likely benign (Jun 13, 2018) | |||
| 16-14672746-G-A | not specified | Uncertain significance (Jul 17, 2023) | ||
| 16-14688174-C-T | not specified | Likely benign (Feb 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLA2G10 | protein_coding | protein_coding | ENST00000438167 | 4 | 22122 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0695 | 0.538 | 125602 | 0 | 1 | 125603 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0287 | 25 | 24.6 | 1.02 | 0.00000123 | 1039 |
| Missense in Polyphen | 8 | 7.7625 | 1.0306 | 337 | ||
| Synonymous | 0.661 | 9 | 11.9 | 0.756 | 7.40e-7 | 338 |
| Loss of Function | -0.679 | 1 | 0.488 | 2.05 | 2.06e-8 | 64 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. Has a powerful potency for releasing arachidonic acid from cell membrane phospholipids. Prefers phosphatidylethanolamine and phosphatidylcholine liposomes to those of phosphatidylserine. {ECO:0000269|PubMed:12161451, ECO:0000269|PubMed:9188469}.;
- Pathway
- 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);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Linoleate metabolism;Glycerophospholipid metabolism;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE;Synthesis of PA;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.123
Haploinsufficiency Scores
- pHI
- 0.138
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.481
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.269
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Pla2g10
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; muscle phenotype;
Gene ontology
- Biological process
- phospholipid metabolic process;phosphatidic acid biosynthetic process;axon guidance;positive regulation of macrophage derived foam cell differentiation;positive regulation of lipid storage;lipid catabolic process;arachidonic acid metabolic process;positive regulation of cellular protein metabolic process;positive regulation of prostaglandin secretion;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;cholesterol homeostasis;regulation of macrophage activation;negative regulation of DNA-binding transcription factor activity;arachidonic acid secretion;lysophospholipid transport;positive regulation of arachidonic acid secretion;negative regulation of cholesterol efflux;cellular response to leukemia inhibitory factor
- Cellular component
- extracellular region;extracellular space
- Molecular function
- phospholipase activity;phospholipase A2 activity;calcium ion binding;phospholipid binding;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)