Inclusive production of $D^*(2010)$ mesons in deep inelastic scattering has been measured with the ZEUS detector at HERA using an integrated luminosity of 81.9 pb$^{-1}$. The decay channel $D^{* +}\to D^0 π^+ $ with $D^0\to K^-π^+$ and corresponding antiparticle decay were used to identify $D^*$ mesons. Differential $D^*$ cross sections with $1.5<Q^2<1000$ GeV$^2$ and $0.02<y<0.7$ in the kinematic region $1.5<p_T(D^*)<15$ GeV and $|η(D^*)|<1.5$ are compared to different QCD calculations incorporating different parameterisations of the parton densities in the proton. The data show sensitivity to the gluon distribution in the proton and are reasonably well described by next-to-leading-order QCD with the ZEUS NLO QCD fit used as the input parton density in the proton. The observed cross section is extrapolated to the full kinematic region in $p_T(D^*)$ and $η(D^*)$ in order to determine the open-charm contribution, $F_2^{\rm charm}(x,Q^2)$, to the proton structure function, $F_2$. Since, at low $Q^2$, the uncertainties of the data are comparable to those from the QCD fit, the measured differential cross sections in $y$ and $Q^2$ should be used in future fits to constrain the gluon density.