Functional investigations of HNF1A identify rare variants as risk factors for type 2 diabetes in the general population

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Variants in HNF1A encoding hepatocyte nuclear factor 1a (HNF-1A) are associated with maturity-onset diabetes of the young form 3 (MODY 3) and type 2 diabetes. We investigated whether functional classification of HNF1A rare coding variants can inform models of diabetes risk prediction in the general population by analyzing the effect of 27 HNF1A variants identified in well-phenotyped populations (n = 4,115). Bioinformatics tools classified 11 variants as likely pathogenic and showed no association with diabetes risk (combined minor allele frequency [MAF] 0.22%; odds ratio [OR] 2.02; 95% CI 0.73-5.60; P = 0.18). However, a different set of 11 variants that reduced HNF-1A transcriptional activity to <60% of normal (wild-type) activity was strongly associated with diabetes in the general population (combined MAF 0.22%; OR 5.04; 95% CI 1.99-12.80; P = 0.0007). Our functional investigations indicate that 0.44% of the population carry HNF1A variants that result in a substantially increased risk for developing diabetes. These results suggest that functional characterization of variants within MODY genes may overcome the limitations of bioinformatics tools for the purposes of presymptomatic diabetes risk prediction in the general population.


  • Laeya Abdoli Najmi
  • Ingvild Aukrust
  • Jason Flannick
  • Janne Molnes
  • Noel Burtt
  • Anders Molven
  • Leif Groop
  • David Altshuler
  • Stefan Johansson
  • Lise Bjørkhaug
  • Pål Rasmus Njølstad
External organisations
  • Haukeland University Hospital
  • University of Bergen
  • Broad Institute
  • Massachusetts General Hospital
  • Bergen University College
  • Harvard University
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Endocrinology and Diabetes
Original languageEnglish
Pages (from-to)335-346
Number of pages12
Issue number2
Publication statusPublished - 2017 Feb 1
Publication categoryResearch