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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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ZNRF3
zinc and ring finger 3
Chromosome 22 · 22q12.1
NCBI Gene: 84133Ensembl: ENSG00000183579.17HGNC: HGNC:18126UniProt: Q9ULT6
73PubMed Papers
20Diseases
0Drugs
7Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
negative regulation of non-canonical Wnt signaling pathwayprotein bindingnegative regulation of canonical Wnt signaling pathwayfrizzled bindinghypertensioncomplex neurodevelopmental disorderprostate carcinomabreast carcinoma
✦AI Summary

ZNRF3 is an E3 ubiquitin ligase that functions as a negative regulator of Wnt/β-catenin signaling by mediating ubiquitination and degradation of Wnt receptor components, including Frizzled and LRP6 1. ZNRF3 acts on both canonical and non-canonical Wnt pathways and serves as a tumor suppressor in intestinal stem cells by restricting Wnt-dependent proliferation 2. Mechanistically, ZNRF3 maintains minimal essential levels of Wnt receptors at the cell membrane 1. Notably, R-spondin ligands antagonize ZNRF3 activity by binding directly to the protein, enabling Wnt pathway amplification independent of LGR4/5/6 receptors; RSPO2 and RNF43 together with ZNRF3 constitute a master developmental switch governing limb specification 3. Beyond Wnt signaling, ZNRF3 regulates other tumor-related proteins including EGFR and BMP pathway components 1. In cancer, loss of RNF43/ZNRF3 drives abnormal β-catenin activation in gastrointestinal tumors and predisposes to hepatocellular carcinoma by impairing liver regeneration and altering lipid metabolism 4. Clinically, higher ZNRF3 expression correlates with improved colorectal carcinoma prognosis and reduced cancer cell proliferation 5, supporting its role as a therapeutic target for Wnt-driven malignancies.

Sources cited
1
ZNRF3 maintains Wnt receptors at minimal levels and regulates EGFR and BMP pathway
PMID: 39551397
2
ZNRF3 function in intestinal stem cell niche and cooperation with RSPO ligands
PMID: 28467820
3
RSPO2 directly antagonizes ZNRF3; RSPO2/RNF43/ZNRF3 master switch in limb development
PMID: 29769720
4
RNF43/ZNRF3 loss causes hepatocellular carcinoma through regeneration defects and lipid metabolic changes
PMID: 35039505
5
ZNRF3 expression predicts better colorectal carcinoma prognosis and suppresses cancer proliferation
PMID: 27822070
Disease Associationsⓘ20
hypertensionOpen Targets
0.49Moderate
complex neurodevelopmental disorderOpen Targets
0.46Moderate
prostate carcinomaOpen Targets
0.44Moderate
breast carcinomaOpen Targets
0.43Moderate
Uterine leiomyomaOpen Targets
0.40Weak
type 2 diabetes mellitusOpen Targets
0.39Weak
congenital heart diseaseOpen Targets
0.37Weak
alcohol drinkingOpen Targets
0.34Weak
androgenetic alopeciaOpen Targets
0.32Weak
breast cancerOpen Targets
0.31Weak
clear cell renal carcinomaOpen Targets
0.31Weak
osteoarthritis, kneeOpen Targets
0.29Weak
renal carcinomaOpen Targets
0.29Weak
osteoarthritisOpen Targets
0.28Weak
adrenal cortex carcinomaOpen Targets
0.28Weak
polycystic ovary syndromeOpen Targets
0.28Weak
Abdominal Aortic AneurysmOpen Targets
0.23Weak
colorectal adenocarcinomaOpen Targets
0.23Weak
vein disorderOpen Targets
0.23Weak
response to xenobiotic stimulusOpen Targets
0.22Weak
Pathogenic Variants7
NM_001206998.2(ZNRF3):c.311T>C (p.Leu104Pro)Pathogenic
ZNRF3-related disorder
★☆☆☆2024→ Residue 104
NM_001206998.2(ZNRF3):c.536C>T (p.Pro179Leu)Pathogenic
ZNRF3-related disorder
★☆☆☆2024→ Residue 179
NM_001206998.2(ZNRF3):c.887G>A (p.Cys296Tyr)Pathogenic
ZNRF3-related disorder
★☆☆☆2024→ Residue 296
NM_001206998.2(ZNRF3):c.920G>A (p.Arg307Gln)Pathogenic
ZNRF3-related disorder
★☆☆☆2024→ Residue 307
NM_001206998.2(ZNRF3):c.956G>A (p.Cys319Tyr)Pathogenic
ZNRF3-related disorder
★☆☆☆2024→ Residue 319
NM_001206998.2(ZNRF3):c.965C>G (p.Pro322Arg)Pathogenic
ZNRF3-related disorder
★☆☆☆2024→ Residue 322
NM_001206998.2(ZNRF3):c.1000C>T (p.Arg334Trp)Pathogenic
ZNRF3-related disorder
★☆☆☆2024→ Residue 334
View on ClinVar ↗
Related Genes
RSPO3Protein interaction99%LGR5Protein interaction98%LGR4Protein interaction98%PCGF3Protein interaction97%LRP5Protein interaction94%FZD3Protein interaction93%
Tissue Expression6 tissues
Heart
100%
Bone Marrow
14%
Brain
3%
Ovary
1%
Liver
1%
Lung
1%
Gene Interaction Network
Click a node to explore
ZNRF3RSPO3LGR5LGR4PCGF3LRP5FZD3
PROTEIN STRUCTURE
Preparing viewer…
PDB8G4Y · 1.41 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.50Moderately Constrained
pLIⓘ
0.97Intolerant
Observed/Expected LoF0.35 [0.25–0.50]
RankingsWhere ZNRF3 stands among ~20K protein-coding genes
  • #6,527of 20,598
    Most Researched73
  • #3,199of 5,498
    Most Pathogenic Variants7
  • #3,037of 17,882
    Most Constrained (LOEUF)0.50 · top quartile
Genes detectedZNRF3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Multi‑layered prevention and treatment of chronic inflammation, organ fibrosis and cancer associated with canonical WNT/β‑catenin signaling activation (Review).
PMID: 29786110
Int J Mol Med · 2018
1.00
2
RNF43 and ZNRF3: Versatile regulators at the membrane and their role in cancer.
PMID: 39551397
Biochim Biophys Acta Rev Cancer · 2024
0.90
3
Non-equivalence of Wnt and R-spondin ligands during Lgr5
PMID: 28467820
Nature · 2017
0.80
4
RSPO2 inhibition of RNF43 and ZNRF3 governs limb development independently of LGR4/5/6.
PMID: 29769720
Nature · 2018
0.70
5
RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.
PMID: 35039505
Nat Commun · 2022
0.60