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Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Frameshift and Copy Number Variants in SACS-Related Neuropathy.

Jun-Hui Yuan¹, Yujiro Higuchi¹, Masahiro Ando¹

¹Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.

Neurology. Genetics

|October 30, 2025

Summary

This study identified SACS gene variants in Japanese patients with inherited peripheral neuropathies (IPNs), revealing a diverse clinical and genetic spectrum. Understanding these SACS-related disorders is crucial for accurate diagnosis and genetic counseling.

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Area of Science:

Genetics
Neurology
Rare Diseases

Background:

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSA) is caused by SACS variants, presenting with spasticity, ataxia, and neuropathy.
Inherited peripheral neuropathies (IPNs) encompass a group of disorders affecting the peripheral nervous system.

Purpose of the Study:

To define the clinical and genetic spectrum of SACS-related IPNs in Japanese patients.
To investigate the contribution of SACS variants to IPN and Charcot-Marie-Tooth (CMT) disease in Japan.

Main Methods:

Targeted gene panel sequencing was performed on 3,353 Japanese patients with suspected IPN or CMT.
Whole-exome sequencing was used for undiagnosed cases.
Copy number variation (CNV) analysis was conducted to detect gene deletions.

Main Results:

Pathogenic SACS variants were confirmed in 9 out of 3,353 patients (0.268%).
The identified variants included frameshift, missense, nonsense, and complete gene deletions.
Clinical presentations ranged from motor and sensory neuropathy to ataxia, cognitive impairment, and postural hypotension, with onset between 1 and 49 years.

Conclusions:

SACS variants contribute to IPN/CMT disease in Japanese patients, exhibiting a heterogeneous genotypic and phenotypic spectrum.
The frequency of SACS gene deletions highlights the importance of CNV analysis in diagnosing SACS-related disorders.