rs358806 — WNT5A

Regulatory variant near WNT5A linked to type 2 diabetes risk via impaired Wnt5a-mediated insulin secretion and adipose inflammation

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WNT5A — The Wnt Signal That Powers Your Beta Cells

WNT5A encodes a member of the Wnt family of secreted signaling proteins that operates primarily through non-canonical (β-catenin-independent) pathways. Inside the pancreas, Wnt5a acts as a direct regulator of insulin secretion; in adipose tissue, the same molecule becomes a pro-inflammatory driver when its natural brake — the adipokine SFRP5 — is lost. A common variant near this gene on chromosome 3p14 alters its regulatory landscape and shifts type 2 diabetes risk in the population.

The Mechanism

rs358806 sits within a long non-coding RNA (LINC02030) approximately 186 kilobases upstream of the WNT5A transcription start site. This positions it in the regulatory hinterland 11 Cis-regulatory elements at this distance are routinely associated with gene expression changes in tissue-specific contexts, including pancreatic islets and adipocytes that controls when and how strongly WNT5A is expressed.

In pancreatic beta cells, Wnt5a promotes insulin secretion through a two-stage signaling cascade: it activates the Wnt-calcium pathway, raising intracellular Ca²⁺ and phosphorylating CamKII22 CamKII
Calcium/calmodulin-dependent protein kinase II — a key sensor of calcium signals in beta cells, which in turn up-regulates FoxO1, PDX-1, and GLUT2. These transcription factors are essential for glucose-stimulated insulin secretion. Wnt5a concentrations are reduced in patients with established type 2 diabetes, and GLP-1 receptor agonist treatment that raises serum Wnt5a correlates directly with improved beta-cell function as measured by HOMA-β33 GLP-1 receptor agonist treatment that raises serum Wnt5a correlates directly with improved beta-cell function as measured by HOMA-β
Xu et al. 2023, PMID 37255814.

In adipose tissue, Wnt5a plays a different role. SFRP5, an anti-inflammatory adipokine secreted by healthy fat cells, normally restrains Wnt5a signaling. When SFRP5 production falls in obesity, uncontrolled Wnt5a activates the JNK pathway, driving macrophage infiltration into adipose tissue and causing glucose intolerance and hepatic steatosis in mouse models. This Science paper44 This Science paper
Ouchi et al. Sfrp5 is an anti-inflammatory adipokine that ameliorates metabolic syndrome. Science, 2010 showed that delivering SFRP5 to obese mice reversed both phenotypes, identifying excess Wnt5a signaling as a causal driver of metabolic dysfunction.

The Evidence

The genetic association was first documented in the landmark WTCCC genome-wide association study55 WTCCC genome-wide association study
Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 2007, which genotyped ~500,000 variants in ~2,000 cases each of bipolar disorder, coronary artery disease, Crohn's disease, rheumatoid arthritis, hypertension, type 1 and type 2 diabetes. rs358806 reached p = 3×10⁻⁶ for type 2 diabetes with an overall OR of 1.16 (95% CI 1.03–1.33). SNPedia genotype analysis places the CC homozygous risk at 1.78-fold relative to the AA reference genotype.

The C allele is the major allele globally (~80%), meaning most people carry at least one copy and about 64% are CC homozygotes. This positions rs358806 as a common, modest-effect risk variant — classically the type most relevant to population-level T2D burden rather than rare high-penetrance disease.

Practical Actions

For CC homozygotes, the key intervention is supporting the insulin secretion pathway that Wnt5a facilitates. Dietary patterns that reduce beta-cell burden — emphasising low-glycaemic foods, adequate protein, and limiting refined carbohydrates — preserve residual secretory capacity. Because Wnt5a in adipose tissue also interfaces with inflammation through the SFRP5 pathway, limiting visceral fat accumulation (particularly through reducing refined carbohydrate and fructose intake) is specifically relevant. Monitoring fasting glucose and HbA1c allows early intervention before beta-cell function deteriorates.

Interactions

TCF7L2 (rs7903146) and this variant act on overlapping pathways — both affect Wnt signalling and beta-cell function. Individuals who carry risk alleles at both loci face a compounded impairment of insulin secretory capacity. The FTO obesity variant (rs9939609) adds an independent adiposity component that can worsen the SFRP5/Wnt5a adipose inflammatory axis. WNT5A also interacts with PPARG-related variants (rs1801282) in the adipocyte differentiation pathway, since WNT5A is a positive regulator of adipogenesis via non-canonical signalling.

Nutrient Interactions

dietary fat altered_metabolism

Genotype Interpretations

What each possible genotype means for this variant.

AA Protected Normal

Reference genotype — baseline type 2 diabetes risk

You carry two copies of the A allele at rs358806, the GRCh38 reference and minor allele (~20% global frequency). SNPedia classifies this as normal diabetes risk with a magnitude score of 1. This genotype is most common in East Asian and Korean populations (23–32% A allele frequency) and least common in African and South Asian populations (~10–11%).

Your Wnt5a regulatory landscape at this locus is not altered by the risk variant, meaning beta-cell Wnt5a signalling and the SFRP5/JNK adipose pathway operate under baseline genetic conditions.

AC One Risk Allele Intermediate

Heterozygous — mildly elevated T2D risk from one C allele

You carry one C allele and one A allele at rs358806. SNPedia assigns this genotype a magnitude of 1.5 with a repute of "bad," reflecting a modest elevation in type 2 diabetes risk relative to the AA reference. About 32% of people of European descent share this genotype (calculated from Hardy-Weinberg equilibrium at ~80% C allele frequency).

One copy of the C risk allele shifts the WNT5A regulatory environment incrementally. The effect is smaller than the CC homozygote but real — the WTCCC finding of OR 1.16 per allele implies an additive effect, and carrying one C allele confers an intermediate position between AA and CC.

CC Two Risk Alleles High Risk

Homozygous risk genotype — 1.78× elevated type 2 diabetes risk

You carry two copies of the C allele at rs358806. SNPedia assigns this genotype a magnitude of 2 with a repute of "bad," corresponding to 1.78-fold increased risk of developing type 2 diabetes. About 64% of Europeans and up to 79% of Africans carry this genotype (based on Hardy-Weinberg from the C allele frequency of ~80% and ~89%, respectively).

Two copies of the C risk allele produce the maximal disruption to the WNT5A regulatory region. In the pancreas, this translates to impaired Wnt5a-mediated insulin secretion via the calcium/CamKII/FoxO1 pathway. In adipose tissue, reduced SFRP5 activity combined with altered Wnt5a expression creates conditions for JNK-driven macrophage infiltration and insulin resistance.

Being the most common genotype does not reduce the individual risk — it means population-level T2D burden is substantially influenced by this locus.