Negative Segregation of a Rare KIF1A Variant in Familial Hyperekplexia Illustrates Pitfalls in Exome Interpretation

Objective To describe a familial exaggerated startle syndrome in which exome sequencing identified a rare candidate variant in KIF1A that was subsequently excluded by segregation analysis. Methods Clinical, electrophysiologic, and genetic investigations were performed in a family with autosomal dominant exaggerated startle responses. Whole-exome sequencing (WES) was conducted in the proband, followed by Sanger segregation analysis in affected relatives. Results A 40-year-old woman presented with lifelong exaggerated startle responses triggered by auditory and tactile stimuli. She had no history of neonatal hypertonia, falls, pyramidal signs, neuropathy, developmental delay, or cerebellar dysfunction. Neurologic examination and nerve conduction studies were normal. Surface electromyography (EMG) demonstrated generalized short-latency startle responses consistent with brainstem hyperexcitability. Symptoms improved substantially with clonazepam. Her daughter exhibited a similar phenotype, and the family history suggested autosomal dominant transmission across three generations. Targeted sequencing of known hyperekplexia-associated genes was negative. WES identified a heterozygous rare missense variant in KIF1A (NM_001244008.1:c.3242A>T; p.Lys1081Ile), initially considered a plausible candidate due to evolutionary conservation, absence from population databases, and deleterious in silico predictions. However, Sanger sequencing demonstrated the absence of the variant in the affected daughter, excluding cosegregation with the disease. Conclusions This report highlights the critical importance of segregation analysis in exome interpretation. Despite biologic plausibility and supportive computational predictions, a lack of cosegregation strongly argued against the pathogenicity of the identified KIF1A variant. The molecular basis of disease in this family remains unresolved.