Elliptic flow (v2) fluctuations in central heavy-ion collisions are direct probes of the fluctuating geometry of the quark-gluon plasma, and, as such, are strongly sensitive to any deviation from spherical symmetry in the shape of the colliding nuclei. I investigate the consequences of nuclear deformation for v2 fluctuations, and I assess whether current models of medium geometry are able to predict and capture such effects. Assuming linear hydrodynamic response between v2 and the eccentricity of the medium, ε2, I perform accurate comparisons between model calculations of ε2 fluctuations and STAR data on cumulants of elliptic flow, in central Au+Au and U+U collisions. From these comparisons, I evince that the most distinct signatures of nuclear deformation appear in the non-Gaussianities of v2 fluctuation, and I show, in particular, that the non-Gaussian v2 fluctuations currently observed in central Au+Au collisions are incompatible with model calculations that implement a quadrupole coefficient of order 12% in the 197 Au nuclei. Finally, I make robust predictions for the behavior of higher-order cumulants of v2 in collisions of non-spherical nuclei.