PLA2G3

phospholipase A2 group III, the group of Phospholipases

Basic information

Region (hg38): 22:31134807-31140508

Links

ENSG00000100078 ∙ NCBI:50487 ∙ OMIM:611651 ∙ HGNC:17934 ∙ Uniprot:Q9NZ20 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLA2G3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G3 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			31	5		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	5	0

Variants in PLA2G3

This is a list of pathogenic ClinVar variants found in the PLA2G3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-31135830-A-C		not specified	Uncertain significance (Oct 01, 2024)
22-31135843-A-T		not specified	Uncertain significance (Mar 07, 2023)
22-31135877-T-C		not specified	Uncertain significance (Apr 23, 2024)
22-31135898-C-T		not specified	Uncertain significance (Nov 07, 2024)
22-31135934-C-T		not specified	Uncertain significance (Mar 19, 2024)
22-31136710-G-A		not specified	Uncertain significance (Jun 18, 2021)
22-31136765-C-T		not specified	Uncertain significance (Jun 24, 2022)
22-31136791-C-A		not specified	Uncertain significance (Jan 09, 2024)
22-31136933-G-A		not specified	Uncertain significance (Feb 16, 2023)
22-31136944-G-A		not specified	Uncertain significance (May 08, 2023)
22-31136975-G-A		not specified	Uncertain significance (Dec 06, 2022)
22-31136985-C-G		not specified	Uncertain significance (Jan 11, 2023)
22-31136993-C-T		not specified	Uncertain significance (Aug 13, 2021)
22-31137010-C-A		not specified	Uncertain significance (Jul 25, 2023)
22-31137010-C-T		not specified	Uncertain significance (Jan 19, 2024)
22-31137013-C-T		not specified	Uncertain significance (Jan 26, 2022)
22-31137034-C-T		not specified	Likely benign (Aug 08, 2022)
22-31137779-T-C		not specified	Likely benign (Aug 02, 2021)
22-31137791-G-A		not specified	Uncertain significance (Jan 26, 2023)
22-31137793-G-A		not specified	Likely benign (Nov 21, 2024)
22-31137817-C-T		not specified	Likely benign (Aug 13, 2021)
22-31137844-C-A		not specified	Uncertain significance (Oct 27, 2022)
22-31137859-T-C		not specified	Uncertain significance (May 09, 2023)
22-31137868-C-T		not specified	Likely benign (Jun 18, 2021)
22-31137888-G-C		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G3	protein_coding	protein_coding	ENST00000215885	7	5799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.56e-11	0.305	124208	3	1537	125748	0.00614

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0713	307	304	1.01	0.0000176	3258
Missense in Polyphen		64	74.826	0.85531		916
Synonymous	-1.16	137	121	1.13	0.00000666	1041
Loss of Function	0.976	19	24.2	0.786	0.00000139	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00992	0.00992
Ashkenazi Jewish	0.0273	0.0273
East Asian	0.000381	0.000381
Finnish	0.00150	0.00148
European (Non-Finnish)	0.00723	0.00715
Middle Eastern	0.000381	0.000381
South Asian	0.00134	0.00134
Other	0.00999	0.00998

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. Shows an 11-fold preference for phosphatidylglycerol over phosphatidylcholine (PC). Preferential cleavage: 1-palmitoyl-2-linoleoyl- phosphatidylethanolamine (PE) > 1-palmitoyl-2-linoleoyl-PC > 1- palmitoyl-2-arachidonoyl-PC > 1-palmitoyl-2-arachidonoyl-PE. Plays a role in ciliogenesis. {ECO:0000269|PubMed:12522102, ECO:0000269|PubMed:20393563}.
• 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);Ras Signaling;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Linoleate metabolism;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0982

Intolerance Scores

• loftool: 0.915
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.88

Haploinsufficiency Scores

• pHI: 0.350
• hipred: N
• hipred_score: 0.112
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0384

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Pla2g3
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hearing/vestibular/ear phenotype; immune system phenotype; embryo phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: acrosome assembly;phospholipid metabolic process;sperm axoneme assembly;lipid catabolic process;lipoxygenase pathway;phosphatidylglycerol acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;mast cell degranulation;arachidonic acid secretion;cilium assembly
• Cellular component: extracellular region;extracellular space;centriole;plasma membrane;mast cell granule
• Molecular function: phospholipase A2 activity;metal ion binding;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)