The gene-level ATXN2L association was primarily due to a single common variant (rs55719896, P = 5.7 × 10−5) within an ATXN2L splice acceptor site and in strong linkage disequilibrium (R2 = 0.99) with an intronic variant (rs9972768) of SH2B1 (a gene with a confirmed role in body mass index (BMI) variability), although none of the rare missense variants of ATXN2L were in linkage disequilibrium (R2 < 0.3) with variants in SH2B1. Further validation of this association is required to implicate ATXN2L in diabetes. Here, ATXN2L is linked to diabetes mellitus.