PLA1A

Chr 3

phospholipase A1 member A

Also known as: PS-PLA1, PSPLA1

NCBI Gene: 51365 ENSG00000144837 UniProt: Q53H76 OMIM: 607460

The protein encoded by this gene is a phospholipase that hydrolyzes fatty acids at the sn-1 position of phosphatidylserine and 1-acyl-2-lysophosphatidylserine. This secreted protein hydrolyzes phosphatidylserine in liposomes. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.24

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.24LOEUF

pLI 0.000

Z-score 0.71

OE 0.83 (0.58–1.24)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.29Z-score

OE missense 0.95 (0.85–1.06)

244 obs / 256.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.83 (0.58–1.24)

0≤0.351.4

Missense OE?0.95 (0.85–1.06)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 18 / 21.6Missense obs/exp: 244 / 256.9Syn Z: -0.23

Background carrier burden — how many people carry a rare variant somewhere in PLA1A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 75

648 rare PASS variants

Rare truncating (LoF)

1 in 470

110 rare PASS variants

Rare synonymous (reference)

1 in 100

245 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PLA1A. 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 110	1 in 1,200
South Asian	~43k	1 in 92	1 in 780
Remaining (unassigned)	~30k	1 in 79	1 in 2,300
European (Finnish)	~27k	1 in 640	1 in 3,800
Admixed American	~22k	1 in 72	1 in 1,200
African / African American	~21k	1 in 85	1 in 610
East Asian	~20k	1 in 89	1 in 1,800
Ashkenazi Jewish	~13k	1 in 200	none seen
Middle Eastern	~2,884	1 in 78	1 in 380

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): 9 of 11 coding exons well covered in gnomAD exomes; exons 4, 11 marginal. Genomes: all 11.? see exons ↓