Highlights We identify the functional connectivity network that characterizes stuttering. We describe the topological similarity of the stuttering cortical network with genetic expression levels from the protein-coding transcriptome data of the Allen Human Brain Atlas. GNPTG significantly co-localizes with the stuttering cortical network. Our findings support that lysosomal-related genes, such as GNPTG, intersect with neurofilament-related genes, which may explain the intriguing link between lysosomal mutations and the presence of stuttering.