PLA2G4E

Chr 15

phospholipase A2 group IVE

NCBI Gene: 123745 ENSG00000188089 UniProt: Q3MJ16

This gene encodes a member of the cytosolic phospholipase A2 group IV family. Members of this family are involved in regulation of membrane tubule-mediated transport. The enzyme encoded by this member of the family plays a role in trafficking through the clathrin-independent endocytic pathway. The enzyme regulates the recycling process via formation of tubules that transport internalized clathrin-independent cargo proteins back to the cell surface. [provided by RefSeq, Jan 2017]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.77

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?

0.77LOEUF

pLI 0.000

Z-score 2.87

OE 0.56 (0.41–0.77)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.14Z-score

OE missense 0.85 (0.79–0.93)

412 obs / 482.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.56 (0.41–0.77)

0≤0.351.4

Missense OE?0.85 (0.79–0.93)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 28 / 49.9Missense obs/exp: 412 / 482.6Syn Z: -0.49

Background carrier burden — how many people carry a rare variant somewhere in PLA2G4E?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 40

1,126 rare PASS variants

Rare truncating (LoF)

1 in 560

184 rare PASS variants

Rare synonymous (reference)

1 in 76

500 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PLA2G4E. 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 56	1 in 600
South Asian	~43k	1 in 44	1 in 690
Remaining (unassigned)	~30k	1 in 38	1 in 360
European (Finnish)	~27k	1 in 110	1 in 2,200
Admixed American	~22k	1 in 50	1 in 490
African / African American	~21k	1 in 50	1 in 560
East Asian	~20k	1 in 49	1 in 730
Ashkenazi Jewish	~13k	1 in 90	1 in 2,200
Middle Eastern	~2,884	1 in 52	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. 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 1 poorly covered. Genomes: 19 of 20 (exon 1 below).? see exons ↓