The analysis of the genotyping rate of individual RED loci revealed one important limitation of repeat expansion detection by exome sequencing: common coding RED loci—such as ATXN2 and HTT, which cause spinocerebellar ataxia 2 and Huntington disease, respectively—may not be sufficiently covered depending on the exome capture kit used: the maximum genotyping rate was 8.8% for ATXN2 targeted by Truseq Exome, and 58.2% for HTT by SureSelect V6. This evidence concerns the gene HTT and spinocerebellar ataxia type 2.