PLA2G2C

protein-coding

phospholipase A2 group IIC, the group of Phospholipases

Gene summary

Predicted to enable calcium ion binding activity; phospholipid binding activity; and signaling receptor binding activity. Predicted to be involved in phosphatidylcholine metabolic process and phosphatidylglycerol metabolic process. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

UBXN10-AS1

MANE transcript

NM_001367969.2

Inheritance

—

ClinVar variants

U:13B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr1:20,161,253-20,186,518

External References & Databases

Ensembl (ENSG00000187980)

Transcript & Mutation Effects

hg38 • Region Span ~25.3 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 PLA2G2C variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367969.2. 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			13 clinvar	3 clinvar		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	3	0	16

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367969.2	RefSeq	NP_001354898.1	4	MANE Select
ENST00000679259.1	Ensembl	ENSP00000504292.1	4	MANE Select
NM_001316722.3	RefSeq	NP_001303651.1	5	Standard
ENST00000247992.5	Ensembl	ENSP00000247992.5	3	Standard

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
lipid catabolic process
arachidonic acid secretion

Molecular Function

phospholipase A2 activity
calcium ion binding
phospholipid binding
calcium-dependent phospholipase A2 activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000429261
Coding exons: 4
Length: 16172
Individuals with no LoFs: 80031
Homozygous LoFs: 5986
Heterozygous LoFs: 38630
Defined: 124647
p: 0.199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0339	81	80.1	1.01	0.00000409	983
Missense (PolyPhen)		30	29.974	1.0009		391
Synonymous	0.0946	34	34.7	0.980	0.00000211	264
Loss of Function	1.23	3	6.33	0.474	2.67e-7	81

Population LoF Frequency

Population	CAF	p-value	Status
African	0.28	0.28	notable
Latino/Admixed American	0.10	0.10	notable
Ashkenazi Jewish	0.21	0.21	notable
East Asian	0.16	0.16	notable
Finnish	0.20	0.20	notable
European (Non-Finnish)	0.19	0.19	notable
South Asian	0.37	0.36	notable
Other	0.19	0.19	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inactive phospholipase. {ECO:0000305}.;

Recessive Scores

pRec: 0.0678

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0206

Gene Damage Prediction

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