PLA2G1B

phospholipase A2 group IB, the group of Phospholipases

Basic information

Region (hg38): 12:120322115-120327779

Previous symbols: [ "PLA2", "PPLA2", "PLA2A" ]

Links

ENSG00000170890NCBI:5319OMIM:172410HGNC:9030Uniprot:P04054AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLA2G1B gene.

  • not_specified (19 variants)
  • not_provided (2 variants)

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. These statistics are base on transcript: NM_000000928.3. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
19
clinvar
1
clinvar
20
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 19 0 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PLA2G1Bprotein_codingprotein_codingENST00000308366 45679
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.01e-100.006601256830641257470.000255
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.70910485.51.220.00000423974
Missense in Polyphen4130.6141.3392321
Synonymous-1.314636.01.280.00000201263
Loss of Function-2.08126.341.892.65e-782

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002100.00210
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0001140.000114
Middle Eastern0.0001090.000109
South Asian0.0002610.000261
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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)