Distinct Clinical Phenotypes in KIF1A-Associated Neurological Disorders Result from Different Amino Acid Substitutions at the Same Residue in KIF1A

KIF1A is a neuron-specific kinesin motor responsible for intracellular transport along axons. Pathogenic KIF1A mutations cause KIF1A-associated neurological disorders (KAND), a spectrum of severe neurodevelopmental and neurodegenerative conditions. While individual KIF1A mutations have been studied, how different substitutions at the same residue affect motor function and disease progression remains unclear. Here, we systematically examine the molecular and clinical consequences of mutations at three key motor domain residues—R216, R254, and R307—using single-molecule motility assays and genotype-phenotype associations. Our findings reveal that mutations at R216 and R254 produce residue-specific effects, with some substitutions partially retaining function, whereas R307 mutations universally abolish motility, likely due to its critical role in microtubule binding. Mutant motor properties correlate with developmental outcomes, with R307 mutations linked to the most sever impairments. These results demonstrate that even single-residue substitutions can lead to distinct molecular and clinical phenotypes, highlighting the finely tuned mechanochemical properties of KIF1A. By establishing residue-specific genotype-phenotype relationships, this work provides fundamental insights into KAND pathogenesis and informs targeted therapeutic strategies.