YPEL3

Chr 16

yippee like 3

NCBI Gene: 83719ENSG00000090238UniProt: P61236

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]

301
ClinVar variants
279
Pathogenic / LP
0.04
pLI score
0
Active trials
Clinical Summary— YPEL3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.04) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
279 Pathogenic / Likely Pathogenic· 22 VUS of 301 total submissions
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?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.54Z-score
OE missense 0.57 (0.46–0.71)
59 obs / 103.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.45 (0.20–1.15)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.57 (0.46–0.71)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.98
0≤1.21.6
LoF obs/exp: 3 / 6.7Missense obs/exp: 59 / 103.0Syn Z: 0.12

ClinVar Variant Classifications

301 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic235
Likely Pathogenic44
VUS22
235
Pathogenic
44
Likely Pathogenic
22
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
————235
Likely Pathogenic
————44
VUS
————22
Likely Benign
————0
Benign
————0
Total—301

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

YPEL3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Frameshift mutations of YPEL3 alter the sensory circuit function in Drosophila.
Kim JH et al.·Dis Model Mech
2020
yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development.
Blanco-Sánchez B et al.·PLoS Genet
2020Case report
Exploring the effect of nsSNPs in human YPEL3 gene in cellular senescence.
Singh A et al.·Sci Rep
2020
Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes.
Vysotskiy M et al.·Genome Med
2021
In search of autophagy biomarkers in breast cancer: Receptor status and drug agnostic transcriptional changes during autophagy flux in cell lines.
Mascia F et al.·PLoS One
2022
Differential biological effects of aromatase inhibitors: Apoptosis, autophagy, senescence and modulation of the hormonal status in breast cancer cells.
Augusto TV et al.·Mol Cell Endocrinol
2021
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
MEOX1-mediated transcriptional regulation of circABHD3 exacerbates hepatic fibrosis through promoting m6A/YTHDF2-dependent YPEL3 mRNA decay to activate β-catenin signaling.
Chen L et al.·PLoS Genet
2025🔓 Open Access
Correction: Upregulation of YPEL3 expression and induction of human breast cancer cell death by microRNAs.
Lee B et al.·Toxicol Res
2024🔓 Open Access
Upregulation of YPEL3 expression and induction of human breast cancer cell death by microRNAs.
Lee B et al.·Toxicol Res
2024🔓 Open Access
YPEL3 expression induces cellular senescence via the Hippo signaling pathway in human breast cancer cells.
Kwon Y et al.·Toxicol Res
2023
YPEL3 Negatively Regulates Endometrial Function via the Wnt/β-Catenin Pathways during Early Pregnancy in Goats.
Liu J et al.·Animals (Basel)
2022🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools