PLA2G4D

Chr 15

phospholipase A2 group IVD

Also known as: cPLA2delta

NCBI Gene: 283748 ENSG00000159337 UniProt: Q86XP0

The phospholipase A2 enzyme family, including PLA2G4D, catalyze the hydrolysis of glycerophospholipids at the sn-2 position and then liberate free fatty acids and lysophospholipids (Chiba et al., 2004 [PubMed 14709560]).[supplied by OMIM, Jun 2009]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.92

LOEUF

GOF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.92LOEUF

pLI 0.000

Z-score 1.98

OE 0.67 (0.49–0.92)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.41Z-score

OE missense 1.05 (0.98–1.14)

490 obs / 465.4 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.67 (0.49–0.92)

0≤0.351.4

Missense OE?1.05 (0.98–1.14)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 28 / 41.8Missense obs/exp: 490 / 465.4Syn Z: 0.38

Background carrier burden — how many people carry a rare variant somewhere in PLA2G4D?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 39

1,125 rare PASS variants

Rare truncating (LoF)

1 in 540

172 rare PASS variants

Rare synonymous (reference)

1 in 62

467 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PLA2G4D. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 48	1 in 390
South Asian	~43k	1 in 46	1 in 240
Remaining (unassigned)	~30k	1 in 34	1 in 450
European (Finnish)	~27k	1 in 92	1 in 380
Admixed American	~22k	1 in 41	1 in 590
African / African American	~21k	1 in 34	1 in 270
East Asian	~20k	1 in 37	1 in 440
Ashkenazi Jewish	~13k	1 in 120	1 in 1,900
Middle Eastern	~2,884	1 in 54	1 in 420

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 19 of 20 coding exons well covered in gnomAD exomes; exon 19 marginal. Genomes: 19 of 20 (exon 4 below).? see exons ↓