The charge current pumped adiabatically through a deformable quantum dot is studied within the Green's function approach. Differently from the non-deformable case, the current shows an undefined parity with respect to the pumping phase ϕ. The unconventional current-phase relation, analyzed in the weak pumping regime, is due to a dynamical phase shift ϕ_D caused by the elastic deformations of the central region (classical phonons). The role of the quality factor Q of the oscillator, the effects induced by a mechanical resonance and the implications for current experiments on molecular systems are also discussed.