PLA2G15
Basic information
Region (hg38): 16:68245304-68261058
Previous symbols: [ "LYPLA3" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (57 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G15 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012320.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 56 | 57 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 56 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLA2G15 | protein_coding | protein_coding | ENST00000219345 | 6 | 15755 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.378 | 0.621 | 125713 | 0 | 20 | 125733 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.751 | 226 | 260 | 0.869 | 0.0000161 | 2642 |
| Missense in Polyphen | 105 | 119.93 | 0.87549 | 1285 | ||
| Synonymous | 1.13 | 95 | 110 | 0.863 | 0.00000666 | 856 |
| Loss of Function | 3.04 | 4 | 17.9 | 0.224 | 8.47e-7 | 194 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000178 | 0.000177 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000133 | 0.000132 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has transacylase and calcium-independent phospholipase A2 activity (PubMed:20410020, PubMed:23958596). Catalyzes the formation of 1-O-acyl-N-acetylsphingosine and the concomitant release of a lyso-phospholipid (PubMed:11790796, PubMed:25727495). Has high activity with 1-palmitoyl-2-oleoyl-sn-glycero-3- phosphocholine (POPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), catalyzing the transfer of oleic acid to N-acetyl- sphingosine. Required for normal phospholipid degradation in alveolar and peritoneal macrophages and in spleen (By similarity). May have weak lysophospholipase activity (PubMed:10092508). {ECO:0000250|UniProtKB:Q8VEB4, ECO:0000269|PubMed:10092508, ECO:0000269|PubMed:11790796, ECO:0000269|PubMed:20410020, ECO:0000269|PubMed:23958596, ECO:0000269|PubMed:25727495}.;
- Pathway
- Glycerophospholipid metabolism - Homo sapiens (human);Lysosome - Homo sapiens (human);Phospholipid Biosynthesis;Metabolism of lipids;Metabolism;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC
(Consensus)
Recessive Scores
- pRec
- 0.159
Intolerance Scores
- loftool
- 0.143
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.56
Haploinsufficiency Scores
- pHI
- 0.0932
- hipred
- Y
- hipred_score
- 0.563
- ghis
- 0.538
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pla2g15
- Phenotype
- homeostasis/metabolism phenotype; cellular 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; normal phenotype; renal/urinary system phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype;
Gene ontology
- Biological process
- phospholipid metabolic process;glycerophospholipid metabolic process;ceramide metabolic process;fatty acid catabolic process;phosphatidylcholine catabolic process;phosphatidylethanolamine catabolic process
- Cellular component
- extracellular region;extracellular space;nucleoplasm;lysosome;membrane;intracellular membrane-bounded organelle;extracellular exosome
- Molecular function
- lysophospholipase activity;phospholipid binding;O-acyltransferase activity;calcium-independent phospholipase A2 activity