We introduce a latent causal variable (LCV) model, under which the genetic correlation between two traits is mediated by a latent variable having a causal effect on each trait. We define trait 1 as partially genetically causal for trait 2 when it is strongly correlated with the causal variable, implying that part of the genetic component of trait 1 is causal for trait 2. We quantify partial causality using the genetic causality proportion. We showed in simulations that LCV has major advantages over MR methods, and we applied it to 52 diseases and complex traits.
