Ptp52F^EP mutants display defects in SNa motor axon guidance. In most segments that display a phenotype, either the posterior or the anterior SNa branch is missing. Occasionally, extra anterior branches are observed. In rare cases, the entire SNa appears to stall at the bifurcation point. Ptp52F^EP mutants exhibit disorganisation of the outer 1D4 bundle, which is often fused with the middle bundle.

Neuronal overexpression of Ptp52F under the control of Scer\GAL4^elav.PLu generates CNS axon guidance defects, with 1D4-positive axon bundles exhibiting breaks and defasciculated regions, and ectopic midline crossing by longitudinal axons observed in 18% of segments.