The embodiments herein relate to transistors having varying thicknesses of gate dielectric layers. The transistor includes a gate dielectric layer between a gate electrode and a substrate. The gate dielectric layer includes a first dielectric portion on the substrate, a second dielectric portion at least partially in the substrate, and a third dielectric portion partially in the substrate between the first and second dielectric portions. The second dielectric portion is thicker than the first dielectric portion. The third dielectric portion is thicker than the first dielectric portion and thinner than the second dielectric portion.