BACKGROUND: CSF1R-related disorder (CSF1R-RD) is a severe autosomal dominant leukoencephalopathy characterized by progressive cognitive, neuropsychiatric, and motor decline. Although genetic testing is widely available, numerous likely pathogenic variants in CSF1R frequently remain classified as variants of uncertain significance (VUS), limiting the option of pre-symptomatic genetic testing or prenatal options for at-risk family members. METHODS: We report a male in his early 50s with progressive leukoencephalopathy and a strong multigenerational family history supported by neuropathological findings consistent with CSF1R-RD. Genetic testing identified a heterozygous CSF1R splice-region variant (c.2763 + 4_2763 + 7del) classified as a VUS. Targeted long-read RNA sequencing of peripheral blood was performed to assess transcript-level consequences. RESULTS: Long-read transcriptomic analysis identified a novel exon 20-skipping isoform absent in pooled controls, accounting for approximately 63% of detected transcripts, with a corresponding reduction in the canonical transcript. Exon skipping (109 bp) results in a frameshift and a premature termination codon in the final exon, predicted to escape nonsense-mediated decay and disrupt the tyrosine kinase domain. These findings establish a direct molecular mechanism of pathogenicity. Functional evidence allowed reclassification of the variant using American College of Medical Genetics and Genomics (ACMG) and Association for Clinical Genomic Science (ACGS) guidelines from VUS to likely pathogenic, enabling definitive molecular diagnosis. CONCLUSIONS: This case demonstrates that targeted long-read transcriptomic sequencing can provide decisive functional evidence to resolve non-canonical splice variants in CSF1R-RD. Focused transcript-level assessment represents a practical adjunct to genomic testing in clinically compelling cases where DNA-based interpretation alone is insufficient. © 2026 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.