Generally speaking, a proline will add a "bend" or kink into the protein secondary structure due to the shape of the proline residue. This is an unusual sort of substitution to make as it can disrupt the shape of the entire protein.

It depends on the protein and the location of the residue in the protein. Has this mutation ever been reported in control individuals ? If this Alanine to Proline change is frequent is the general population, it has most probably no effect on protein function...