By using the self-consistent Born approximation, we investigate disorder effect induced by the short-range impurities on the band gap in two-dimensional Dirac systems with the higher order terms in momentum. Starting from the Bernevig-Hughes-Zhang (BHZ) model, we calculate the density of states as a function of the disorder strength. We show that due to quadratic corrections to the Dirac Hamiltonian, the band gap is always affected by the disorder even if the system is gapless in the clean limit. Finally, we explore the disorder effects by using an advanced effective Hamiltonian describing the side maxima of the valence subband in HgTe quantum wells. We show that the band gap and disorder-induced topological phase transition in the real structures may differ significantly from those predicted within the BHZ model.