It has been shown that a Weyl point in a superconducting nanostructure may give rise to a Weyl disk where two quantum states are almost degenerate in a two-dimensional manifold in the parametric space. This opens up the possibility of a holonomic quantum manipulation: A transformation of the wave function upon an adiabatic change of the parameters within the degenerate manifold. In this paper, we investigate in detail the opportunities for holonomic manipulation in Weyl disks. We compute the connection at the manifold in quasiclassical approximation to show it is Abelian and can be used for a phase gate. To provide a closed example of quantum manipulation that includes a state preparation and readout, we augment the holonomic gate with a change of parameters that brings the system out of the degenerate subspace. For numerical illustrations, we use a finite value of quasiclassical parameter and exact quantum dynamics. We investigate the fidelity of an example gate for different execution times. We evaluate the decoherence rate and show it can be made small to ensure a wide frequency range where an adiabatic manipulation remains coherent.