Homozygous RFC1 AAGGG Repeat Expansions Are Common in Idiopathic Peripheral Neuropathy

Biallelic intronic AAGGG repeat expansions in RFC1 cause cerebellar ataxia with neuropathy and vestibular areflexia syndrome and may also contribute to isolated sensory neuropathy. The clinical significance of both heterozygous and homozygous (biallelic) RFC1 expansions in more diverse patient populations remains unclear-partly due to the absence of accurate, user-friendly computational pipelines specifically tailored for tandem repeat analysis.

To discern the relationship between RFC1 expansions and idiopathic peripheral neuropathy (iPN), we performed whole-genome sequencing (WGS) followed by polymerase chain reaction (PCR)-based confirmation in a large, well-characterized US cohort consisting of 788 patients with iPN (369 pure small fiber neuropathy (SFN), 266 sensorimotor, 144 pure sensory, and 9 pure motor). We developed an integrative pipeline combining ExpansionHunter Denovo and Expansion Hunter coupled with unsupervised clustering to reliably detect and genotype RFC1 expansions from short-read WGS data, achieving 97.2% concordance with repeat-primed PCR-based validation.

Biallelic RFC1 expansions were present in only 1 out of 778 controls but present in 18 out of 788 (2.3%) patients with iPN (Fisher's exact p = 7 × 10^-5), including 6.9% (10/144) of pure sensory, 1.1% (4/369) of SFN, and 1.5% (4/266) of sensorimotor neuropathy. These data indicate that motor nerve involvement should not exclude patients from RFC1 repeat screening. Monoallelic expansions were observed at a nominally higher frequency in iPN than in controls (9.1% vs 7.2%), but this difference did not reach statistical significance (Fisher's exact p = 0.17). We also found no evidence of second mutations or expansions on the other allele among monoallelic carriers.

Our approach provides a robust, cost-effective method for detecting RFC1 expansions from WGS data. Our findings indicate that homozygous (biallelic) AAGGG repeat expansions in RFC1 contribute to development of iPN. Heterozygous expansions may also confer disease risk, but future studies are needed to assess this observation and explore any phenotypic differences with biallelic cases. ANN NEUROL 2026;100:95-108.