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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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WNT9B
Wnt family member 9B
Chromosome 17 · 17q21.32
NCBI Gene: 7484Ensembl: ENSG00000158955.11HGNC: HGNC:12779UniProt: E7EPC3
37PubMed Papers
0Diseases
0Drugs
2Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
midbrain dopaminergic neuron differentiationreceptor ligand activitynon-canonical Wnt signaling pathwaycanonical Wnt signaling pathway
✦AI Summary

WNT9B is a secreted Wnt ligand that activates canonical (β-catenin-dependent) and non-canonical Wnt signaling pathways 1. As a frizzled receptor ligand, WNT9B plays critical roles in embryonic development, particularly in kidney and urogenital tract morphogenesis, where it activates signaling cascades in metanephric mesenchyme to induce tubulogenesis and acts upstream of WNT4 in tubule formation 1. WNT9B is essential for craniofacial development and palatal fusion; mutations cause nonsyndromic cleft lip and palate through epigenetic mechanisms involving retrotransposon-mediated transcriptional interference 2. In adult tissues, endothelial cell-derived WNT9B maintains hepatic metabolic zonation and supports liver regeneration via β-catenin signaling; Wnt activators rescue liver function in acute liver failure models 3. Clinically, homozygous WNT9B variants are associated with bilateral renal agenesis/hypoplasia/dysplasia in humans 4, and common WNT9B polymorphisms associate with Mayer-Rokitansky-Küster-Hauser syndrome risk through gene-gene interactions 5. Genome-wide association studies identify WNT9B variants linked to cardiac age acceleration and adverse cardiovascular outcomes 6. These findings establish WNT9B as a developmental regulator with therapeutic potential in regenerative medicine and organ dysfunction.

Sources cited
1
WNT9B is a secreted ligand driving canonical and non-canonical Wnt signaling; critical for kidney, heart, and craniofacial development
PMID: 39616032
2
Endothelial WNT9B maintains hepatic metabolic zonation and liver regeneration; Wnt agonists rescue acute liver failure
PMID: 36220068
3
WNT9B deficiency caused by retrotransposon-mediated epigenetic silencing causes nonsyndromic cleft lip and palate in A/WySn mice
PMID: 25257647
4
Homozygous WNT9B variants associate with bilateral renal agenesis/hypoplasia/dysplasia in human families
PMID: 34145744
5
WNT9B polymorphisms associate with Mayer-Rokitansky-Küster-Hauser syndrome with gene-gene interactions
PMID: 26075712
6
WNT9B variants linked to cardiac age acceleration and adverse cardiovascular outcomes in genome-wide association study
PMID: 39148824
7
WNT9B expressed in craniofacial arches, heart, and fin buds during vertebrate development; mutations cause cleft lip
PMID: 18694329
Pathogenic Variants2
NM_003396.3(WNT9B):c.949G>A (p.Gly317Arg)Likely pathogenic
Cystic renal dysplasia;Chronic kidney disease
☆☆☆☆2021→ Residue 317
NM_003396.3(WNT9B):c.11dup (p.Pro5fs)Likely pathogenic
Renal dysplasia;Chronic kidney disease;Renal hypoplasia
☆☆☆☆2021→ Residue 5
View on ClinVar ↗
Related Genes
PORCNProtein interaction97%WNT5AProtein interaction96%WLSProtein interaction96%NOTUMProtein interaction94%WIF1Protein interaction92%CER1Protein interaction92%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
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WNT9BPORCNWNT5AWLSNOTUMWIF1CER1
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt O14905
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.68LoF Tolerant
pLIⓘ
0.23Tolerant
Observed/Expected LoF0.42 [0.27–0.68]
RankingsWhere WNT9B stands among ~20K protein-coding genes
  • #10,722of 20,598
    Most Researched37
  • #4,482of 5,498
    Most Pathogenic Variants2
  • #5,109of 17,882
    Most Constrained (LOEUF)0.68
Genes detectedWNT9B
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Single-cell spatial transcriptomics reveals a dynamic control of metabolic zonation and liver regeneration by endothelial cell Wnt2 and Wnt9b.
PMID: 36220068
Cell Rep Med · 2022
1.00
2
WNT9A and WNT9B in Development and Disease.
PMID: 39616032
Differentiation · 2025
0.90
3
Characterization of SHH, SOX3, WNT3A and WNT9B Proteins in Human Non-Syndromic Cleft Lip and Palate Tissue.
PMID: 37366674
Dent J (Basel) · 2023
0.80
4
Zebrafish Wnt9b synteny and expression during first and second arch, heart, and pectoral fin bud morphogenesis.
PMID: 18694329
Zebrafish · 2008
0.70
5
Epigenetic mechanism causes Wnt9b deficiency and nonsyndromic cleft lip and palate in the A/WySn mouse strain.
PMID: 25257647
Birth Defects Res A Clin Mol Teratol · 2014
0.60