Earlier theoretical calculations of the Seebeck coefficient of mayenite electride have shown that electrons are the major type of charge carriers, while experimental measurements show that the carriers are holes. We investigated the interplay between the experimentally observed deformation of Ca-Al-O cages in mayenite electride and its transport properties to reveal the reasons for this discrepancy. We found that the deformation of individual cages lifts the degeneracy of the electride subsystem and induces the localization of electrons in these interstices. This leads to significant changes in the band structure near the Fermi level, accompanied by splitting of the electride states into two subsystems separated by an indirect energy gap. As a result, the sign of the Seebeck coefficient changes and becomes positive, indicating that holes are the main type of charge carriers in accordance with the experimental observations. This outcome confirms that the mayenite electride subsystem cannot be considered as a homogeneous gas of free electrons but should be considered as partially localized electrons that can move through the crystal together with local deformations.