In the present paper we investigate the set $Sigma_J$ of all $J$-self-adjoint extensions of a symmetric operator $S$ with deficiency indices $<2,2>$ which commutes with a non-trivial fundamental symmetry $J$ of a Krein space $(mathfrak{H}, [cdot,cdot
])$, SJ=JS. Our aim is to describe different types of $J$-self-adjoint extensions of $S$. One of our main results is the equivalence between the presence of $J$-self-adjoint extensions of $S$ with empty resolvent set and the commutation of $S$ with a Clifford algebra ${mathcal C}l_2(J,R)$, where $R$ is an additional fundamental symmetry with $JR=-RJ$. This enables one to construct the collection of operators $C_{chi,omega}$ realizing the property of stable $C$-symmetry for extensions $AinSigma_J$ directly in terms of ${mathcal C}l_2(J,R)$ and to parameterize the corresponding subset of extensions with stable $C$-symmetry. Such a situation occurs naturally in many applications, here we discuss the case of an indefinite Sturm-Liouville operator on the real line and a one dimensional Dirac operator with point interaction.
