You can try setting equal upper and lower bounds for those variables. For example,
lb = [3, -inf,5];
ub = [3,inf,5];
sets x(1) = 3 and x(3) = 5, while leaving x(2) unconstrained.
Of course, it might be even better to just reformulate your problem to have fewer variables, but I know that is sometimes difficult.
MATLAB mathematical toolbox documentation