rs4712523

This is a intron variant variant in the CDKAL1 gene.

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GWAS Catalog Trait Associations (6)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

type 2 diabetes mellitus

Takeuchi F et al. “Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population.” Diabetes 58(7):1690-9 (2009)
Allele G
OR 1.27
p 7.0e-20
N 1,022
Large GWAS
East Asian
Rung J et al. “Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia.” Nature Genetics 41(10):1110-5 (2009)
Allele G
OR 1.20
p 2.0e-12
N 1,376
Large GWAS
European

systolic blood pressure

Surendran P et al. “Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.” Nature Genetics 52(12):1314-1332 (2020)
Allele A
OR 0.18
p 5.0e-15
N 1,164,961
Meta-analysisLarge GWAS
European

histidine measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.02
p 5.0e-12
N 450,015
Large GWAS
multi-ancestry

pulse pressure measurement

Surendran P et al. “Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.” Nature Genetics 52(12):1314-1332 (2020)
Allele A
OR 0.09
p 7.0e-9
N 1,164,961
Meta-analysisLarge GWAS
European

diastolic blood pressure

Surendran P et al. “Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.” Nature Genetics 52(12):1314-1332 (2020)
Allele A
OR 0.10
p 9.0e-9
N 810,865
Meta-analysisLarge GWAS
European

hypertension

Surendran P et al. “Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.” Nature Genetics 52(12):1314-1332 (2020)
Allele A
OR 5.71
p 1.0e-8
N 1,164,961
Meta-analysisLarge GWAS
European
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Research that mentions this SNP (2)

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Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets
AssociationN=84Dayeh TA et al.(2013)· Diabetologia

Of 40 SNPs previously associated with type 2 diabetes, 19 (48%) introduce or remove CpG sites. In 84 human pancreatic islet donors, all 16 analyzed CpG-SNPs showed statistically significant differential DNA methylation (p≤2.3×10⁻⁵). Several CpG-SNPs including rs391300 (SRR), rs5945326 (DUSP9), rs11708067 (ADCY5), rs5015480 (HHEX), rs13266634 (SLC30A8), rs1801214 (WFS1), rs564398 (CDKN2A), and rs2237895 (KCNQ1) were associated with differential gene expression, alternative splicing, or hormone secretion, suggesting DNA methylation-mediated mechanisms linking genetic variants to type 2 diabetes pathogenesis.

Traits studied:Glucagon secretionInsulin contentInsulin secretionType 2 diabetes
PubMedDOIMetascience Observatory
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Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus
AssociationN=3,000Chirag J. Patel et al.(2013)· Human Genetics

This systematic study screened 18 T2D-associated SNPs and 5 environmental factors (trans-β-carotene, cis-β-carotene, γ-tocopherol, heptachlor epoxide, PCB170) for gene-environment interactions using NHANES data (1999-2000, 2001-2002). The strongest interaction was between rs13266634 (SLC30A8) and trans-β-carotene: in subjects with low trans-β-carotene levels, the per-risk-allele OR was 1.8 (95% CI 1.3-2.6), 40% higher than the marginal effect, and this interaction withstood Bonferroni correction (p = 0.006, FDR 1.5%). Four interactions total achieved FDR < 20%, suggesting that nutrient levels modify genetic risk for T2D.

Traits studied:Type 2 diabetes mellitus
PubMedDOIMetascience Observatory

About CDKAL1

The protein encoded by this gene is a member of the methylthiotransferase family. The function of this gene is not known. Genome-wide association studies have linked single nucleotide polymorphisms in an intron of this gene with susceptibilty to type 2 diabetes. [provided by RefSeq, May 2010]

View all CDKAL1 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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