Single nucleotide polymorphisms (SNPs) close to the VPS13C, C2CD4A and C2CD4B genes on chromosome 15q are associated with impaired fasting glucose and increased risk of type 2 diabetes. eQTL analysis revealed an association between possession of risk (C) alleles at a previously-implicated causal SNP, rs7163757, and lowered VPS13C and C2CD4A levels in islets from female (n=40; p<0.041) but not male subjects. Explored using promoter-reporter assays in β and other cell lines, the risk variant at rs7163757, lowered enhancer activity. Mice deleted for Vps13c selectively in the β cell were generated by crossing animals bearing a floxed allele at exon 1 to mice expressing Cre recombinase under Ins1 promoter control (Ins1Cre). Whilst Vps13c^fl/fl::Ins1Cre (βVps13cKO) mice displayed normal weight gain compared to control littermates, deletion of Vps13c had little effect on glucose tolerance. Pancreatic histology revealed no significant change in β cell mass in KO mice versus controls and glucose-stimulated insulin secretion from isolated islets was not altered in vitro between control and βVps13cKO mice. However, a tendency was observed in female null mice for lower insulin levels and β cell function (HOMA-B) in vivo. Furthermore, glucose-stimulated increases in intracellular free Ca²⁺ were significantly increased in islets from female KO mice, suggesting impaired Ca²⁺ sensitivity of the secretory machinery. The present data thus provide evidence for a limited role for changes in VPS13C expression in conferring altered disease risk at this locus, particularly in females, and suggest that C2CD4A may also be involved.