PLA2G2A
phospholipase A2 group IIA, the group of Phospholipases
Basic information
Region (hg38): 1:19975431-19980416
Previous symbols: [ "PLA2B", "PLA2L" ]
Links
Phenotypes
GenCC
Source:
- colorectal cancer (No Known Disease Relationship), mode of inheritance: AD
- colorectal cancer (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (19 variants)
- PLA2G2A-related_disorder (3 variants)
- not_provided (2 variants)
- Familial_colorectal_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001395463.1. 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 | 2 | |||||
| missense | 17 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 17 | 3 | 3 |
Highest pathogenic variant AF is 0.0000378065
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLA2G2A | protein_coding | protein_coding | ENST00000375111 | 4 | 5008 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0973 | 0.781 | 125720 | 0 | 28 | 125748 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.684 | 64 | 81.4 | 0.787 | 0.00000480 | 945 |
| Missense in Polyphen | 16 | 31.237 | 0.51221 | 371 | ||
| Synonymous | -0.563 | 36 | 32.0 | 1.13 | 0.00000188 | 259 |
| Loss of Function | 1.18 | 2 | 4.80 | 0.417 | 2.03e-7 | 66 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000275 | 0.000275 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000176 | 0.000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides (PubMed:2925633). Thought to participate in the regulation of phospholipid metabolism in biomembranes including eicosanoid biosynthesis. Independent of its catalytic activity, acts as a ligand for integrins (PubMed:18635536, PubMed:25398877). Binds to and activates integrins ITGAV:ITGB3, ITGA4:ITGB1 and ITGA5:ITGB1 (PubMed:18635536, PubMed:25398877). Binds to a site (site 2) which is distinct from the classical ligand-binding site (site 1) and induces integrin conformational changes and enhanced ligand binding to site 1 (PubMed:25398877). Induces cell proliferation in an integrin-dependent manner (PubMed:18635536). {ECO:0000269|PubMed:18635536, ECO:0000269|PubMed:25398877, ECO:0000269|PubMed:2925633}.;
- 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);Celecoxib Pathway, Pharmacodynamics;Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;Indomethacin Action Pathway;MicroRNAs in cardiomyocyte hypertrophy;Eicosanoid Synthesis;Spinal Cord Injury;Cardiac Hypertrophic Response;Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Antimicrobial peptides;Innate Immune System;Immune System;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;Glypican 1 network;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.195
Intolerance Scores
- loftool
- 0.829
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.95
Haploinsufficiency Scores
- pHI
- 0.280
- hipred
- N
- hipred_score
- 0.212
- ghis
- 0.414
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.971
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pla2g2a
- Phenotype
- neoplasm;
Gene ontology
- Biological process
- phospholipid metabolic process;phosphatidic acid biosynthetic process;positive regulation of macrophage derived foam cell differentiation;lipid catabolic process;antimicrobial humoral response;low-density lipoprotein particle remodeling;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;phosphatidic acid metabolic process;arachidonic acid secretion;positive regulation of inflammatory response;defense response to Gram-positive bacterium;positive regulation of ERK1 and ERK2 cascade
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;secretory granule;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- 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)