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Updated: Jan 29, 2026

Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
Biallelic KARS pathogenic variants cause an early-onset progressive leukodystrophy.
Masayuki Itoh1, Hongmei Dai1, Shin-Ichi Horike2
1Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, Japan.
Genetic abnormalities in lysyl-tRNA synthetase (KARS) cause severe progressive leukodystrophy in children. This study identifies novel KARS variants linked to neurodevelopmental defects, epilepsy, and motor impairments, highlighting KARS
Area of Science:
- Genetics and Molecular Biology
- Neuroscience
- Biochemistry
Background:
- Leukodystrophies are severe, progressive neurodevelopmental disorders often leading to premature death.
- Aminoacyl-t-RNA synthetase (ARS) gene abnormalities are increasingly linked to leukodystrophies and leukoencephalopathies.
- ARS enzymes are crucial for protein synthesis but can have non-canonical roles in transcription and translation.
Observation:
- Seven patients from five families presented with severe developmental delay, hypotonia, deafness, and inability to speak.
- Progressive symptoms included intractable epilepsy and nystagmus, alongside characteristic metabolic (lactate/pyruvate) and neuroimaging findings (white matter calcification/abnormalities).
- Whole-exome sequencing identified novel pathogenic variants in the lysyl-tRNA synthetase (KARS) gene in all affected individuals.
Findings:
- All patients harbored homozygous or compound heterozygous KARS variants, including a recurrent [c.1786C>T, p.Leu596Phe] mutation.
- Disrupted lysyl-tRNA synthetase (LysRS) proteins exhibited reduced enzymatic activity and abnormal central nervous system development in Xenopus models.
- LysRS demonstrated non-canonical roles as an immune response inducer and in transcriptional regulation.
Implications:
- Pathogenic KARS variants, particularly the recurrent [c.1786C>T, p.Leu596Phe] mutation, are strongly associated with severe progressive leukodystrophy.
- The complex, non-canonical functions of LysRS likely contribute to the severe neurological phenotypes observed in patients.
- Further research into KARS-related diseases is warranted to understand the spectrum of KARS-associated disorders and potential therapeutic targets.
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