PLA2G1B
phospholipase A2 group IB, the group of Phospholipases
Basic information
Region (hg38): 12:120322115-120327779
Previous symbols: [ "PLA2", "PPLA2", "PLA2A" ]
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 PLA2G1B 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 | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 7 | 1 | 1 |
Variants in PLA2G1B
This is a list of pathogenic ClinVar variants found in the PLA2G1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-120322242-T-C | not specified | Uncertain significance (Aug 21, 2023) | ||
| 12-120322272-T-C | not specified | Uncertain significance (Aug 03, 2022) | ||
| 12-120322275-C-T | Benign (May 30, 2018) | |||
| 12-120325006-T-C | not specified | Uncertain significance (Feb 10, 2023) | ||
| 12-120325009-A-G | not specified | Uncertain significance (Oct 13, 2023) | ||
| 12-120325048-G-A | not specified | Uncertain significance (Aug 22, 2023) | ||
| 12-120325071-G-A | Likely benign (Jun 01, 2018) | |||
| 12-120325891-C-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 12-120326012-C-T | not specified | Uncertain significance (Nov 15, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLA2G1B | protein_coding | protein_coding | ENST00000308366 | 4 | 5679 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.01e-10 | 0.00660 | 125683 | 0 | 64 | 125747 | 0.000255 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.709 | 104 | 85.5 | 1.22 | 0.00000423 | 974 |
| Missense in Polyphen | 41 | 30.614 | 1.3392 | 321 | ||
| Synonymous | -1.31 | 46 | 36.0 | 1.28 | 0.00000201 | 263 |
| Loss of Function | -2.08 | 12 | 6.34 | 1.89 | 2.65e-7 | 82 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00210 | 0.00210 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000114 | 0.000114 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000261 | 0.000261 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides, this releases glycerophospholipids and arachidonic acid that serve as the precursors of signal molecules. {ECO:0000269|PubMed:19297324}.;
- 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);Angiogenesis overview;Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;p38 mapk signaling pathway;eicosanoid metabolism;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Linoleate metabolism;Glycerophospholipid metabolism;fc epsilon receptor i signaling in mast cells;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE;Synthesis of PA;Fc-epsilon receptor I signaling in mast cells;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.632
Intolerance Scores
- loftool
- 0.831
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.383
- hipred
- N
- hipred_score
- 0.348
- ghis
- 0.453
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.983
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pla2g1b
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; liver/biliary system phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- activation of MAPK activity;innate immune response in mucosa;neutrophil mediated immunity;fatty acid biosynthetic process;phospholipid metabolic process;phosphatidic acid biosynthetic process;actin filament organization;signal transduction;positive regulation of cell population proliferation;positive regulation of calcium ion transport into cytosol;lipid catabolic process;leukotriene biosynthetic process;antibacterial humoral response;neutrophil chemotaxis;activation of phospholipase A2 activity;interleukin-8 production;cellular response to insulin stimulus;intracellular signal transduction;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;positive regulation of transcription by RNA polymerase II;regulation of glucose import;phosphatidylcholine metabolic process;positive regulation of fibroblast proliferation;arachidonic acid secretion;positive regulation of protein secretion;positive regulation of immune response;defense response to Gram-positive bacterium;positive regulation of NF-kappaB transcription factor activity;antimicrobial humoral immune response mediated by antimicrobial peptide
- Cellular component
- extracellular region;extracellular space;cytosol;cell surface;secretory granule
- Molecular function
- phospholipase A2 activity;signaling receptor binding;calcium ion binding;phospholipid binding;bile acid binding;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)