PLA2G2A

phospholipase A2 group IIA, the group of Phospholipases

Basic information

Region (hg38): 1:19975430-19980416

Previous symbols: [ "PLA2B", "PLA2L" ]

Links

ENSG00000188257 ∙ NCBI:5320 ∙ OMIM:172411 ∙ HGNC:9031 ∙ Uniprot:P14555 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• colorectal cancer (No Known Disease Relationship), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLA2G2A gene.

• Inborn genetic diseases (4 variants)
• not provided (2 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.

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					1	1
missense			4		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	2

Variants in PLA2G2A

This is a list of pathogenic ClinVar variants found in the PLA2G2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-19975708-C-T		PLA2G2A-related disorder	Benign (Jun 17, 2019)
1-19975733-T-C		not specified	Uncertain significance (Jun 07, 2023)
1-19975747-T-A		not specified	Uncertain significance (Mar 04, 2024)
1-19975823-T-C		not specified	Uncertain significance (Dec 03, 2021)
1-19978068-C-A		not specified	Uncertain significance (Aug 28, 2023)
1-19978121-G-A		not specified	Likely benign (Oct 02, 2023)
1-19978381-G-A		not specified	Uncertain significance (Jul 19, 2023)
1-19978407-C-T		not specified	Likely benign (Sep 16, 2021)
1-19978419-CCA-C		Familial colorectal cancer	Pathogenic (Sep 01, 1997)
1-19978433-G-A		PLA2G2A-related disorder	Benign (Oct 25, 2019)
1-19978455-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-19978469-C-G		PLA2G2A-related disorder	Benign (Nov 19, 2019)
1-19978510-G-A		PLA2G2A-related disorder	Benign (Feb 26, 2019)
1-19978513-C-T		PLA2G2A-related disorder	Likely benign (Aug 07, 2019)
1-19978756-C-T			Benign (Apr 23, 2018)

GnomAD

Source: gnomAD

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: dbNSFP

• 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)