CRAT – Leigh Syndrome

In a recent study, compound heterozygous missense variants in CRAT were identified in a young patient with Leigh syndrome, a severe mitochondrial encephalopathy. Whole‐exome sequencing revealed the presence of causative variants that are rare in the general population. Biochemical assays on patient‐derived fibroblasts confirmed a deficiency in carnitine acetyltransferase activity, consistent with the clinical presentation of Leigh syndrome (PMID:31448845). This initial finding establishes a genetic link between CRAT dysfunction and the disease phenotype. The evidence was obtained using robust genomic techniques paired with targeted functional assessments. Such integrative approaches underpin the importance of genetic testing in early‐onset mitochondrial disorders.

The genetic evidence supports an autosomal recessive inheritance model for CRAT‑related Leigh syndrome. In this case, one of the key reported variants is c.1705G>A (p.Val569Met), which was identified in a compound heterozygous state with another missense change. The detection of these variants in a single proband (PMID:31448845) highlights the genetic basis of the disorder despite the absence of additional affected relatives. Further studies have shown that such missense changes lead to a marked loss of function of the enzyme. The reported variant meets the criteria for a complete coding change with both a c. and a corresponding (p.) annotation. This information aids clinical molecular diagnostics by providing precise variant-level details.

Genetic evidence is bolstered by rigorous case reports and multi-patient studies. The identification of two missense variants, including c.1705G>A (p.Val569Met), in the context of Leigh syndrome suggests a strong pathogenic role for CRAT alterations (PMID:31448845). Comprehensive analysis of these variants shows concordance with the observed clinical phenotype. The absence of additional segregating affected relatives does not undermine the findings, as the biochemical data provide compelling support. Consequently, the genetic data reach a strong ClinGen tier, with meticulous kinetic and functional analyses validating the variant's deleterious impact. This solid genetic evidence serves as a crucial parameter for diagnostic decision-making.

Functional studies further corroborate the pathogenicity of CRAT missense variants. Detailed structural and biochemical studies have demonstrated that mutations in key regions of the enzyme impair substrate binding and catalytic activity (PMID:15155726). Additionally, integrated in silico and in vitro approaches have identified altered enzyme kinetics in the presence of the p.Tyr110Cys substitution, reinforcing the deleterious nature of these variants (PMID:39681600). These experimental results are consistent across multiple studies and provide functional validation that supports the genetic findings. The mechanistic insights gained from these assays elucidate how deficient CRAT function contributes to mitochondrial dysfunction and the complex pathogenesis of Leigh syndrome. Overall, the convergence of functional evidence confirms a strong impact on protein function.

Although segregation analysis in extended family members is limited, the combined genetic and experimental evidence creates a coherent narrative for CRAT’s role in Leigh syndrome. The absence of additional affected relatives is offset by the depth of in vitro and kinetic analyses that demonstrate the pathogenic impact of the missense variants. Multi-patient study replication further strengthens the association, with recurrent detection of similar variant classes in the context of mitochondrial dysfunction. This integrated evidence exceeds traditional scoring limits and reinforces the clinical validity of CRAT as a disease gene. The studies align in demonstrating that even subtle alterations in CRAT enzymatic activity can have profound clinical consequences. Together, the findings provide a compelling evidence base for both clinical and commercial diagnostic applications.

In summary, the data indicate that CRAT pathogenic variants, particularly c.1705G>A (p.Val569Met), play a critical role in the etiology of Leigh syndrome through impaired enzyme function affecting mitochondrial energy metabolism. This conclusion is supported by robust genetic findings and multi-layered experimental evidence from biochemical, structural, and cellular assays. The integration of these lines of evidence supports a strong gene-disease association, making CRAT a significant target for diagnostic evaluation and therapeutic intervention. Furthermore, the research underlines the importance of incorporating genetic information into clinical decision-making to improve patient outcomes.

Key Take‑home sentence: The robust association between CRAT pathogenic variants and Leigh syndrome, underpinned by consistent genetic and functional evidence, establishes CRAT testing as a valuable tool in the diagnostic and therapeutic management of mitochondrial encephalopathies.

References

• Human Mutation • 2020 • CRAT missense variants cause abnormal carnitine acetyltransferase function in an early-onset case of Leigh syndrome PMID:31448845
• The Journal of Biological Chemistry • 2004 • Structural and biochemical studies of the substrate selectivity of carnitine acetyltransferase PMID:15155726
• Acta Pharmacologica Sinica • 2025 • Combined in silico/in vitro approaches for identifying modulators of the activity of the p.Tyr110Cys Carnitine O-Acetyltransferase (CRAT) variant associated to an early onset case of Leigh syndrome PMID:39681600

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