Whole-Genome and Long-Read Sequencing Identify a Novel Mechanism inRFC1Resulting in CANVAS Syndrome

Abstract

ObjectivesCerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS) results from biallelic intronic pentanucleotide repeats inRFC1.We describe an adult male proband with progressive imbalance, cerebellar atrophy, somatosensory neuronopathy, and absence of peripheral vestibular function for whom clinical testing demonstrated a heterozygousRFC1expansion consistent with an unaffected carrier.MethodsWe performed whole-genome sequencing (WGS) on peripheral blood DNA samples from the proband and his unaffected mother. We performed DNA long-read sequencing and synthesized complementary DNA from RNA using peripheral blood from the proband.ResultsWGS confirmed the maternally inheritedRFC1expansion and identified a rare, nonsenseRFC1variant: c.C1147T; p.R383X in the proband but not the maternal DNA sample.RFC1variants were confirmed intranswith long-read sequencing. Functional studies demonstrated the absence of complementary DNA (cDNA) transcript from the c.C1147T; p.R383X variant supporting nonsense-mediated decay of this transcript.DiscussionWe report an adult with CANVAS due to compound heterozygous pathogenicRFC1variants: the pathogenic intronic pentanucleotide expansion confirmed intranswith a nonsense variant. This report represents a novel molecular mechanism for CANVAS. Sequencing forRFC1should be considered for adults meeting clinical criteria for the CANVAS phenotype if only a heterozygous pathogenicRFC1expansion is identified.