PLA2G4F

phospholipase A2 group IVF, the group of Phospholipases|C2 domain containing phospholipases

Basic information

Region (hg38): 15:42139034-42156636

Links

ENSG00000168907 ∙ NCBI:255189 ∙ ∙ HGNC:27396 ∙ Uniprot:Q68DD2 ∙ 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 PLA2G4F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G4F 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			68	1		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	2	0

Variants in PLA2G4F

This is a list of pathogenic ClinVar variants found in the PLA2G4F region.

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

Position	Type	Phenotype	Significance	ClinVar
15-42142003-C-G		not specified	Uncertain significance (May 23, 2024)
15-42142003-C-T		not specified	Uncertain significance (Nov 30, 2022)
15-42142015-C-T		not specified	Uncertain significance (Jun 02, 2023)
15-42142025-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-42142030-T-G		not specified	Uncertain significance (Apr 09, 2024)
15-42142058-T-C		not specified	Uncertain significance (Sep 27, 2021)
15-42142121-A-G		not specified	Uncertain significance (Nov 03, 2023)
15-42142195-C-T		not specified	Uncertain significance (Jan 12, 2024)
15-42142545-C-T		not specified	Uncertain significance (Jan 04, 2024)
15-42142569-A-G		not specified	Uncertain significance (May 30, 2023)
15-42142584-G-C		not specified	Uncertain significance (Mar 02, 2023)
15-42142590-C-T		not specified	Uncertain significance (Apr 22, 2024)
15-42142591-G-A		not specified	Uncertain significance (Feb 28, 2024)
15-42142593-G-A		not specified	Uncertain significance (May 25, 2022)
15-42142638-A-T		not specified	Uncertain significance (Jun 27, 2022)
15-42142640-G-C		not specified	Uncertain significance (Sep 13, 2023)
15-42142651-C-T		not specified	Uncertain significance (Nov 10, 2022)
15-42142662-C-A		not specified	Uncertain significance (Apr 07, 2022)
15-42142671-G-C		not specified	Uncertain significance (Nov 18, 2023)
15-42144000-T-C		not specified	Uncertain significance (Nov 30, 2021)
15-42144039-A-G		not specified	Uncertain significance (Apr 28, 2023)
15-42144060-G-T		not specified	Uncertain significance (Apr 08, 2024)
15-42144070-C-G		not specified	Uncertain significance (Nov 27, 2023)
15-42144097-A-C		not specified	Uncertain significance (Dec 01, 2022)
15-42144103-G-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G4F	protein_coding	protein_coding	ENST00000382396	20	15508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.15e-27	0.000892	125524	1	223	125748	0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.532	530	497	1.07	0.0000292	5436
Missense in Polyphen		129	130.33	0.98979		1574
Synonymous	-0.148	212	209	1.01	0.0000127	1737
Loss of Function	0.597	44	48.5	0.908	0.00000261	490

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00161
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000599	0.000598
Finnish	0.000236	0.000231
European (Non-Finnish)	0.000854	0.000844
Middle Eastern	0.000599	0.000598
South Asian	0.00219	0.00206
Other	0.000985	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position. Has higher enzyme activity for phosphatidylethanolamine than phosphatidylcholine (By similarity). {ECO:0000250}.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Platelet activation - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Fc gamma R-mediated phagocytosis - Homo sapiens (human);Ether lipid metabolism - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Long-term depression - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Necroptosis - 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);MAPK signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);MAPK Signaling Pathway;Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC;Acyl chain remodelling of PE (Consensus)

Recessive Scores

• pRec: 0.0982

Intolerance Scores

• loftool: 0.813
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.1

Haploinsufficiency Scores

• pHI: 0.0630
• hipred: N
• hipred_score: 0.455
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g4f
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: prostaglandin biosynthetic process;phospholipid metabolic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;glycerophospholipid catabolic process;arachidonic acid secretion;cellular response to antibiotic;cellular response to organic cyclic compound
• Cellular component: cytoplasm;lysosomal membrane;cytosol;vesicle;ruffle membrane
• Molecular function: lysophospholipase activity;phospholipase A2 activity;calcium ion binding;calcium-dependent phospholipid binding;phospholipase A1 activity;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)