Many genetic variants are of unknown significance (VUS). Efficient and accurate electronic health record (EHR) phenotyping, having facilitated genome-wide association studies, could identify patients with VUSs who exhibit phenotypic features that might indicate pathogenicity of those variants. Identifying and following up with these patients could improve their healthcare, and assist in improving genetic variant categorization. With further assessment, these methods, combined with other data, could be used to identify phenotypes in patients with VUSs, URVs, or CPVs, which in turn could facilitate the functional categorization of those variants as either pathogenic or benign.