Six variant sets significantly associated with T2D (p ≤ 1.46 × 10–6); pLOF variants in GIGYF1, GCK, HNF1A and TNRC6B and damaging missense variants in GCK and PAM (Fig. 2, Table 2 and Supplementary Table 2). Here, HNF1A is linked to type 2 diabetes mellitus.