Novel homozygous SYNE1 missense variant in late onset autosomal recessive cerebellar ataxia 1: a case report.

Abstract

SYNE1 ataxia is a rare representative of autosomal recessive hereditary cerebellar ataxias (ARCAs). It was originally described in the Beauce region of Quebec as a pure cerebellar form of ataxia. Later, more complex phenotypes with a wide range of extra-cerebellar neurological and non-neurological dysfunctions were discovered in other geographical locations. SYNE1 deficiency was predominantly linked to nonsense and frameshift variants; however, missense variants in the gene SYNE1 have also been described as causative for this type of ataxia. We here describe a case of an adult female patient with a phenotype of progressive ataxic features over 15 years, combined with spastic paraparesis. Non-neurological symptoms were not present. The family history was negative, and the case was classified as sporadic. However, the parents of the patient were related to both grandmothers, being cousins. DNA was sequenced using the Illumina HiSeq/Nova Seq system, and the variant c.23413A>G; p.Arg7805Gly in the gene SYNE1 was found in a homozygous state (NM_033071.4; NP_149062.2). This missense variant has not been described in the literature and is not listed in the relevant databases. This homozygous substitution resulted in an amino acid change, arginine for glycine, in a highly conserved region of the SYNE1 gene. According to ACMG/ACGS guidelines, the criteria PM2+PM3_supporting+PP3 were applied, which classified the substitution c.23413A>G; p.Arg7805Gly as "a variant of uncertain significance." The calculated effect of this substitution is mostly pathogenic based on several in silico prediction programs. The presence of spastic paraparesis grades this case as an ataxic complex syndrome. This is the first SYNE1 ataxia patient of Polish origin with a novel missense variant described with full clinical and MRI data.