Rare Genetic Variants of Large Effect Influence Risk of Type 1 Diabetes.

Most replicated genetic determinants for type 1 diabetes are common (minor allele frequency [MAF] >5%). We aimed to identify novel rare or low-frequency (MAF <5%) single nucleotide polymorphisms with large effects on risk of type 1 diabetes. We undertook deep imputation of genotyped data followed by genome-wide association testing and meta-analysis of 9,358 type 1 diabetes case and 15,705 control subjects from 12 European cohorts. Candidate variants were replicated in a separate cohort of 4,329 case and 9,543 control subjects. Our meta-analysis identified 27 independent variants outside the MHC, among which 3 were novel and had MAF <5%. Three of these variants replicated with P replication < 0.05 and P combined < P discovery In silico analysis prioritized a rare variant at 2q24.3 (rs60587303 [C], MAF 0.5%) within the first intron of STK39, with an effect size comparable with those of common variants in the INS and PTPN22 loci (combined [from the discovery and replication cohorts] estimate of odds ratio [ORcombined] 1.97, 95% CI 1.58-2.47, P combined = 2.9 × 10-9). Pharmacological inhibition of Stk39 activity in primary murine T cells augmented effector responses through enhancement of interleukin 2 signaling. These findings provide insight into the genetic architecture of type 1 diabetes and have identified rare variants having a large effect on disease risk. © 2020 by the American Diabetes Association.

Citation

Vincenzo Forgetta, Despoina Manousaki, Roman Istomine, Stephanie Ross, Marie-Catherine Tessier, Luc Marchand, Min Li, Hui-Qi Qu, Jonathan P Bradfield, Struan F A Grant, Hakon Hakonarson, DCCT/EDIC Research Group, Andrew D Paterson, Ciriaco Piccirillo, Constantin Polychronakos, J Brent Richards. Rare Genetic Variants of Large Effect Influence Risk of Type 1 Diabetes. Diabetes. 2020 Apr;69(4):784-795

Mesh Tags

PMID: 32005708

search → result