Accurate and reliable identification of the RTF between microphones with respect to a desired source is an essential component in the design of microphone array beamformers, specifically the MVDR criterion. Since an accurate estimation of the RTF in a noisy and reverberant environment is a cumbersome task, we aim at leveraging prior knowledge of the acoustic enclosure to robustify the RTF estimation by learning the RTF manifold. In this paper, we present a novel robust RTF identification method, tested and trained with real recordings, which relies on learning the RTF manifold using a GCN to infer a robust representation of the RTF in a confined area, and consequently enhance the beamformer's performance.