PLA2G2F

phospholipase A2 group IIF, the group of Phospholipases

Basic information

Region (hg38): 1:20139323-20150381

Links

ENSG00000158786 ∙ NCBI:64600 ∙ OMIM:616793 ∙ HGNC:30040 ∙ Uniprot:Q9BZM2 ∙ 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 PLA2G2F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G2F 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	26	1	0

Variants in PLA2G2F

This is a list of pathogenic ClinVar variants found in the PLA2G2F region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20139463-C-A		not specified	Uncertain significance (Oct 16, 2024)
1-20139506-C-T		not specified	Uncertain significance (Oct 28, 2024)
1-20139521-T-C		not specified	Uncertain significance (Apr 30, 2024)
1-20140166-G-A		not specified	Likely benign (Oct 07, 2024)
1-20140183-A-C		not specified	Uncertain significance (Oct 04, 2024)
1-20140210-C-T		not specified	Uncertain significance (Jul 11, 2023)
1-20143460-C-T		not specified	Uncertain significance (Apr 06, 2022)
1-20143472-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-20143475-A-T		not specified	Uncertain significance (Jan 02, 2024)
1-20143484-G-A		not specified	Uncertain significance (May 05, 2023)
1-20143528-C-G		not specified	Uncertain significance (Jan 21, 2025)
1-20143529-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-20143532-G-T		not specified	Uncertain significance (Oct 20, 2024)
1-20143548-G-A		not specified	Uncertain significance (Sep 14, 2022)
1-20143560-G-T		not specified	Uncertain significance (Apr 15, 2024)
1-20143579-T-G		not specified	Uncertain significance (May 20, 2024)
1-20144580-G-T		not specified	Uncertain significance (Mar 05, 2025)
1-20144585-G-A		not specified	Uncertain significance (Jun 18, 2024)
1-20144613-A-T		not specified	Uncertain significance (Oct 12, 2022)
1-20144622-C-A		not specified	Uncertain significance (Jan 18, 2023)
1-20144654-A-G		not specified	Uncertain significance (Dec 04, 2024)
1-20144672-A-T		not specified	Uncertain significance (Mar 02, 2023)
1-20144674-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-20148213-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-20148219-C-A		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G2F	protein_coding	protein_coding	ENST00000375102	5	11061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000271	0.181	125700	0	46	125746	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.284	134	125	1.07	0.00000713	1376
Missense in Polyphen		47	45.254	1.0386		507
Synonymous	0.475	47	51.3	0.916	0.00000339	385
Loss of Function	-0.304	8	7.12	1.12	3.01e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.00	0.00
East Asian	0.00130	0.00120
Finnish	0.00	0.00
European (Non-Finnish)	0.0000636	0.0000615
Middle Eastern	0.00130	0.00120
South Asian	0.000324	0.000294
Other	0.000896	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in lipid mediator production in inflammatory conditions, by providing arachidonic acid to downstream cyclooxygenases and lipoxygenases (By similarity). Phospholipase A2, which catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides (PubMed:11112443). Hydrolyzes phosphatidylethanolamine more efficiently than phosphatidylcholine, with only a modest preference for arachidonic acid versus linoelic acid at the sn-2 position. Comparable activity toward 1-palmitoyl-2-oleoyl-phosphatidylserine vesicles to that toward 1-palmitoyl-2-oleoyl-phosphatidylglycerol (By similarity). Hydrolyzes phosphatidylglycerol versus phosphatidylcholine with a 15-fold preference (PubMed:11112443). {ECO:0000250|UniProtKB:Q9QZT4, ECO:0000269|PubMed:11112443}.
• 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 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)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.604
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.146
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g2f

Gene ontology

• Biological process: phospholipid metabolic process;phosphatidic acid biosynthetic process;biological_process;lipid catabolic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;negative regulation of T cell proliferation;innate immune response;arachidonic acid secretion
• Cellular component: extracellular region;cytosol;plasma membrane
• 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)