PLA2G2E

protein-coding

phospholipase A2 group IIE, the group of Phospholipases

Gene summary

Enables A2-type glycerophospholipase activity and calcium ion binding activity. Predicted to be involved in phosphatidylcholine metabolic process and phosphatidylglycerol metabolic process. Predicted to act upstream of or within low-density lipoprotein particle remodeling. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014589.3

Inheritance

—

ClinVar variants

U:32B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr1:19,920,009-19,923,617

External References & Databases

Ensembl (ENSG00000188784)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLA2G2E variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 33

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014589.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar	1 clinvar		33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	1	0	33

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014589.3	RefSeq	NP_055404.1	4	MANE Select
ENST00000375116.3	Ensembl	ENSP00000364257.3	4	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

phospholipid metabolic process
phosphatidic acid biosynthetic process
inflammatory response
lipid catabolic process
low-density lipoprotein particle remodeling

Molecular Function

phospholipase A2 activity
calcium ion binding
phospholipid binding
calcium-dependent phospholipase A2 activity
phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine)

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375116
Coding exons: 4
Length: 3609
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125744
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.286	87	94.8	0.917	0.00000609	918
Missense (PolyPhen)		29	40.495	0.71615		399
Synonymous	0.783	34	40.3	0.843	0.00000292	275
Loss of Function	0.0280	7	7.08	0.989	3.01e-7	80

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00031	0.00031	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. Has a preference for arachidonic-containing phospholipids.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.640
RVIS EVS: 0.13
RVIS percentile EVS: 63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.564

Gene Damage Prediction

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