In conclusion, our study revealed phenotypic and genotypic signatures in FCD subtype IIa and IIb despite a close relationship of affected mTOR pathway genes, i.e., DEPDC5, NPRL3, and MTOR, as well as converging histopathology findings, e.g., cortical dyslamination and dysmorphic neurons. Here, DEPDC5 is linked to fleck corneal dystrophy.