YPEL3

Chr 16

yippee like 3

NCBI Gene: 83719 ENSG00000090238 UniProt: P61236 OMIM: 609724

YPEL3 encodes a protein that binds metal ions and is involved in regulating cellular senescence and proliferation/apoptosis in myeloid precursor cells. Mutations in YPEL3 have not been definitively associated with human disease. The gene shows tolerance to loss-of-function variation (pLI 0.04, LOEUF 1.15).

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable metal ion binding activity. Involved in positive regulation of cellular senescence. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.15

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.15LOEUF

pLI 0.042

Z-score 1.32

OE 0.45 (0.20–1.15)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.54Z-score

OE missense 0.57 (0.46–0.71)

59 obs / 103.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.45 (0.20–1.15)

0≤0.351.4

Missense OE?0.57 (0.46–0.71)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 3 / 6.7Missense obs/exp: 59 / 103.0Syn Z: 0.12

Background carrier burden — how many people carry a rare variant somewhere in YPEL3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 350

191 rare PASS variants

Rare truncating (LoF)

1 in 14,000

23 rare PASS variants

Rare synonymous (reference)

1 in 860

81 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for YPEL3. 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 1,200	1 in 13,000
South Asian	~43k	1 in 440	≈ 1 in 14,000
Remaining (unassigned)	~30k	1 in 410	≈ 1 in 30,000
European (Finnish)	~27k	1 in 1,400	none seen
Admixed American	~22k	1 in 610	≈ 1 in 22,000
African / African American	~21k	1 in 510	≈ 1 in 6,000
East Asian	~20k	1 in 380	none seen
Ashkenazi Jewish	~13k	none seen	≈ 1 in 13,000
Middle Eastern	~2,884	≈ 1 in 960	none seen

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): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓