Type 2 diabetes (T2DM) affects over 400 million people worldwide, a majority of whom are overweight or obese. In the past few decades, the prevalence of T2DM has dramatically increased, putting millions of people at risk for comorbidities and premature death. With approximately 2 billion adults overweight, understanding why some individuals who are overweight progress to T2DM while others do not is of critical importance. However, even with increasing sample sizes and genetic data thanks to genome wide association studies and meta-analyses, only a small portion of the genetic risk for T2DM has been explained. Modeling common complex diseases via monogenic causes of disease allows for the removal of many confounding factors. The obesity-related ciliopathies Alström (AS) and Bardet-Biedl (BBS) Syndromes provide a unique model for understanding why some individuals develop T2DM under very similar conditions. Both ciliopathies are characterized by early onset truncal obesity, but only AS presents with childhood T2DM. Here we endeavor to understand the relative lack of T2DM seen in individuals with BBS despite similar rates and types of obesity. To accomplish this, we first analyzed glucose and insulin data from carriers of the most common disease-causing variant of BBS finding that carriers maintained lower blood glucose levels than matched controls. Next, to elucidate whether this enhanced glycemic control was due to changes in beta cell function, we assessed various measures of glucose metabolism and insulin secretion in beta cells depleted of BBS1. Here we found that although BBS1 does not have a clear role in GCK activity or intracellular calcium level in response to glucose, there is increased beta cell response to incretin stimulation in cells lacking BBS1. Finally, we investigate pathways that are not linked to the primary cilium to uncover potential extraciliary roles of BBS1 in the beta cell. Together this work provides evidence of additional sources of variability in glucose homeostasis in both rare disease and the general population.