When combining rare variants, all functional variants may either be assumed to influence the trait in the same direction, or some may be allowed to have opposite directions of effects. A biochemical argument can be made that most of non-synonymous variants are loss-of-function hypomorphs, while gain-of-function variants are infrequent. However, some genes (e.g., PCSK968) have variants of both kinds. Several tests allow for rare variants to have opposite effects on the trait (e.g., Step-up69, C-alpha, replication-based test70, SKAT). These tests are based either on the analysis of over-dispersion or on explicit linear models that determine the contribution of a variant to a score based on the direction of effect observed in the data.
