This paper presents a method on how to estimate main effects of gene representation. This estimate can be used not only to understand the domination of genes in the representation but also to design the mutation rate in genetic algorithms (GAs). A new approach of dynamic mutation rate is proposed by integrating the information of the main effects into the genes. By introducing the proposed method in GAs, both solution quality and solution stability can be improved in solving a set of parametrical test functions. The algorithm was applied to two illustrative applications to evaluate the performance of the proposed method, where the first application is on solving uncapacitated facility location problems and the next is on optimal power flow problems, which are employed. Results indicate that the proposed method yields significantly better results than the existing methods.