PLA2G4D
phospholipase A2 group IVD, the group of Phospholipases|C2 domain containing phospholipases
Basic information
Region (hg38): 15:42067009-42094562
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (140 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G4D gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178034.4. 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 | 4 | |||||
| missense | 130 | 10 | 140 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 130 | 13 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLA2G4D | protein_coding | protein_coding | ENST00000290472 | 20 | 27546 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.63e-14 | 0.849 | 119823 | 174 | 5751 | 125748 | 0.0238 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.406 | 490 | 465 | 1.05 | 0.0000277 | 5232 |
| Missense in Polyphen | 118 | 109.41 | 1.0785 | 1345 | ||
| Synonymous | 0.376 | 200 | 207 | 0.967 | 0.0000127 | 1670 |
| Loss of Function | 1.98 | 28 | 41.8 | 0.669 | 0.00000197 | 476 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0655 | 0.0654 |
| Ashkenazi Jewish | 0.0108 | 0.0109 |
| East Asian | 0.107 | 0.108 |
| Finnish | 0.00863 | 0.00849 |
| European (Non-Finnish) | 0.00726 | 0.00723 |
| Middle Eastern | 0.107 | 0.108 |
| South Asian | 0.0238 | 0.0231 |
| Other | 0.0167 | 0.0168 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position (PubMed:14709560). May have a substrate specificity for linoleic acid at the sn-2 position (PubMed:14709560). {ECO:0000269|PubMed:14709560}.;
- Pathway
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Platelet activation - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Fc gamma R-mediated phagocytosis - Homo sapiens (human);Ether lipid metabolism - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Long-term depression - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Necroptosis - 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);MAPK signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);MAPK Signaling Pathway;Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC;Acyl chain remodelling of PE;Synthesis of PA
(Consensus)
Recessive Scores
- pRec
- 0.0982
Intolerance Scores
- loftool
- 0.952
- rvis_EVS
- 1.61
- rvis_percentile_EVS
- 95.93
Haploinsufficiency Scores
- pHI
- 0.114
- hipred
- N
- hipred_score
- 0.246
- ghis
- 0.386
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.101
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Pla2g4d
- Phenotype
Gene ontology
- Biological process
- phospholipid metabolic process;phosphatidic acid biosynthetic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;glycerophospholipid catabolic process
- Cellular component
- cytoplasm;cytosol;membrane
- Molecular function
- lysophospholipase activity;phospholipase A2 activity;calcium ion binding;calcium-dependent phospholipid binding;phospholipase A1 activity;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)