PLA2G5

phospholipase A2 group V, the group of Phospholipases

Basic information

Region (hg38): 1:20028178-20091911

Links

ENSG00000127472 ∙ NCBI:5322 ∙ OMIM:601192 ∙ HGNC:9038 ∙ Uniprot:P39877 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• late-adult onset retinitis pigmentosa (Limited), mode of inheritance: AR
• familial benign flecked retina (Supportive), mode of inheritance: AR
• familial benign flecked retina (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fleck retina, familial benign	AR	General	The clinical relevance of the condition is unclear	Ophthalmologic	8703867; 17502520; 22137173

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLA2G5 gene.

• not provided (94 variants)
• Familial benign flecked retina (4 variants)
• not specified (2 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G5 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	16	2	19
missense			52			52
nonsense			3			3
start loss						0
frameshift			4			4
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region			1	3	1	5
non coding				7	1	8
Total	0	0	62	23	3

Variants in PLA2G5

This is a list of pathogenic ClinVar variants found in the PLA2G5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20084838-GC-CT			Uncertain significance (Jun 15, 2023)
1-20084839-C-T		not specified	Benign (Jan 31, 2024)
1-20084845-C-G			Likely benign (Jun 19, 2023)
1-20084846-C-T			Uncertain significance (Dec 27, 2022)
1-20084847-C-T			Uncertain significance (Apr 24, 2023)
1-20084886-G-A			Likely benign (Jan 02, 2024)
1-20084890-C-T			Likely benign (Dec 11, 2023)
1-20086076-C-T			Likely benign (Apr 24, 2022)
1-20086083-G-A			Uncertain significance (Sep 02, 2021)
1-20086083-G-C			Uncertain significance (Mar 13, 2023)
1-20086085-G-A			Uncertain significance (Oct 13, 2022)
1-20086089-C-T			Uncertain significance (Nov 07, 2022)
1-20086090-T-C			Likely benign (Jul 28, 2023)
1-20086100-G-A			Uncertain significance (Nov 14, 2021)
1-20086103-G-C			Uncertain significance (Aug 04, 2023)
1-20086104-G-T			Uncertain significance (Sep 13, 2022)
1-20086112-G-T			Uncertain significance (Mar 14, 2022)
1-20086128-T-C			Uncertain significance (Dec 07, 2021)
1-20086130-G-A			Uncertain significance (Jan 12, 2021)
1-20086133-A-G			Uncertain significance (Oct 19, 2020)
1-20086144-G-T			Uncertain significance (Feb 15, 2023)
1-20086146-A-AG			Uncertain significance (Jun 14, 2022)
1-20086150-C-T			Likely benign (Oct 23, 2023)
1-20086152-C-G			Uncertain significance (Nov 13, 2023)
1-20086165-C-T			Likely benign (Nov 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G5	protein_coding	protein_coding	ENST00000375108	4	63012

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000538	0.460	125729	0	16	125745	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.273	82	89.3	0.919	0.00000569	889
Missense in Polyphen		24	33.227	0.72231		358
Synonymous	0.969	30	37.5	0.799	0.00000264	263
Loss of Function	0.391	7	8.21	0.853	4.36e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. This isozyme hydrolyzes more efficiently L-alpha-1-palmitoyl-2-oleoyl phosphatidylcholine than L-alpha-1-palmitoyl-2-arachidonyl phosphatidylcholine, L- alpha-1-palmitoyl-2-arachidonyl phosphatidylethanolamine, or L- alpha-1-stearoyl-2-arachidonyl phosphatidylinositol. May be involved in the production of lung surfactant, the remodeling or regulation of cardiac muscle.
• Disease: DISEASE: Fleck retina, familial benign (FRFB) [MIM:228980]: An autosomal recessive condition associated with a distinctive retinal appearance and no apparent visual or electrophysiologic deficits. Affected individuals are asymptomatic, but fundus examination reveals a striking pattern of diffuse, yellow-white, fleck-like lesions extending to the far periphery of the retina but sparing the foveal region. {ECO:0000269|PubMed:22137173}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• 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);Spinal Cord Injury;VEGFA-VEGFR2 Signaling Pathway;Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;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;Arachidonic acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.588
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.155
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g5
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: phospholipid metabolic process;phosphatidic acid biosynthetic process;platelet activating factor biosynthetic process;positive regulation of phospholipase activity;lipid catabolic process;leukotriene biosynthetic process;response to cytokine;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;regulation of macrophage activation;arachidonic acid secretion;negative regulation of inflammatory response;response to cAMP;positive regulation of ERK1 and ERK2 cascade
• Cellular component: extracellular region;Golgi apparatus;plasma membrane;cell surface;perinuclear region of cytoplasm
• Molecular function: phospholipase A2 activity;calcium ion binding;phospholipid binding;heparin binding;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)