Rare genetic variants are expected to play an important role in disease and several statistical methods have been developed to test for disease association with rare variants, including variance-component tests. These tests however deal only with binary or continuous phenotypes and it is not possible to take advantage of a suspected heterogeneity between subgroups of patients. To address this issue, we extended the popular rare-variant association test SKAT to compare more than two groups of individuals. Simulations under different scenarios were performed that showed gain in power in presence of genetic heterogeneity and minor lack of power in absence of heterogeneity. An application on whole-exome sequencing data from patients with early- or late-onset moyamoya disease also illustrated the advantage of our SKAT extension. Genetic simulations and SKAT extension are implemented in the R package Ravages available on GitHub ( https://github.com/genostats/Ravages ).