PLA2G4E

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

Basic information

Region (hg38): 15:41981393-42051190

Links

ENSG00000188089 ∙ NCBI:123745 ∙ ∙ HGNC:24791 ∙ Uniprot:Q3MJ16 ∙ 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 PLA2G4E gene.

• Inborn genetic diseases (34 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G4E 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					2	2
missense			32	2	3	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	5

Variants in PLA2G4E

This is a list of pathogenic ClinVar variants found in the PLA2G4E region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41983798-C-T		not specified	Uncertain significance (Dec 13, 2021)
15-41983804-G-A		not specified	Uncertain significance (Jan 09, 2024)
15-41983957-C-T		not specified	Uncertain significance (May 01, 2022)
15-41984453-C-T		not specified	Likely benign (Jan 10, 2022)
15-41984465-T-C		not specified	Uncertain significance (May 27, 2022)
15-41984511-G-C		not specified	Uncertain significance (Oct 26, 2023)
15-41984518-C-T		not specified	Uncertain significance (Jun 29, 2022)
15-41984589-C-T		not specified	Uncertain significance (Oct 17, 2023)
15-41984605-G-A			Benign (May 21, 2018)
15-41985877-T-C		not specified	Uncertain significance (Aug 21, 2023)
15-41985883-C-T		not specified	Uncertain significance (Dec 21, 2023)
15-41985919-T-A		not specified	Uncertain significance (Dec 27, 2023)
15-41985924-T-C		not specified	Uncertain significance (May 23, 2023)
15-41987262-G-A		not specified	Uncertain significance (Oct 06, 2022)
15-41987267-G-A		not specified	Uncertain significance (Feb 03, 2023)
15-41987366-G-A		not specified	Uncertain significance (Oct 03, 2023)
15-41989421-T-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
15-41989453-A-G		not specified	Uncertain significance (Jan 31, 2024)
15-41989489-T-A		not specified	Uncertain significance (Apr 12, 2022)
15-41989522-C-T		not specified	Uncertain significance (Dec 03, 2021)
15-41989529-C-T		not specified	Uncertain significance (Sep 29, 2022)
15-41990170-G-A			Benign (May 21, 2018)
15-41990225-C-T		not specified	Uncertain significance (Dec 20, 2023)
15-41990229-C-T		not specified	Uncertain significance (Nov 23, 2021)
15-41990234-C-A		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G4E	protein_coding	protein_coding	ENST00000399518	20	69609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.32e-13	0.998	124946	0	94	125040	0.000376

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	412	483	0.854	0.0000269	5646
Missense in Polyphen		138	184.71	0.7471		2204
Synonymous	-0.489	207	198	1.04	0.0000116	1651
Loss of Function	2.87	28	49.9	0.561	0.00000287	513

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000997
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000401	0.000384
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000352	0.000344
Middle Eastern	0.000401	0.000384
South Asian	0.000131	0.000131
Other	0.00182	0.00181

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position. {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;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)

Intolerance Scores

• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.8

Haploinsufficiency Scores

• pHI: 0.0953
• hipred: N
• hipred_score: 0.422
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.344

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g4e

Gene ontology

• Biological process: phospholipid metabolic process;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;glycerophospholipid catabolic process
• Cellular component: cytoplasm;lysosomal membrane;cytosol
• 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)