Molecular genetics & genomic medicine · 2025
A Novel Missense Variant of the ABCD1 Gene in X-Linked Adrenoleukodystrophy in Chinese Family.
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Fu Hongxia, Han Lu, Liu Xianhong, He Bin, He Pei, Hu Junjian
Аннотация
BACKGROUND: We identified a novel ABCD1 variant (c.773T>G, p.Leu258Arg, NM_000033.4) in a Chinese pedigree affected by X-linked adrenoleukodystrophy (X-ALD). This missense variant in exon 1 is predicted to be pathogenic and likely constitutes the genetic basis of the disease phenotype in this family.
METHODS: ABCD1 gene sequencing was performed in the Chinese pedigree. The pathogenicity of identified variants was assessed using computational prediction tools. Subcellular localization studies were conducted, and very-long-chain fatty acid (VLCFA) levels were quantified in patient-derived samples.
RESULTS: Sequencing analysis identified a hemizygous missense variant in the ABCD1 gene (c.773T>G; p.Leu258Arg). In silico pathogenicity prediction using SIFT and PolyPhen-2 algorithms classified the p.Leu258Arg substitution as deleterious. Functional characterization revealed that the p.Leu258Arg variant impairs the peroxisomal membrane localization of the ABCD1 protein. Consistent with the established role of ABCD1 in peroxisomal β-oxidation, individuals harboring this variant exhibited significantly elevated serum levels of VLCFA. Specifically, the C26:0/C22:0 ratio was elevated 2.8-fold compared to control values, confirming impaired VLCFA metabolism.
CONCLUSION: In accordance with the "Standards and Guidelines for the Interpretation of Sequence Variants" established by the American College of Medical Genetics and Genomics (ACMG), we assessed the pathogenicity of the novel ABCD1 gene variant c.773T>G. This variant meets the following ACMG evidence criteria: PM1 (located within a critical functional domain or mutational hotspot known to lack benign variation); PM2 (absent or observed at very low frequency in population databases e.g., gnomAD, EXAC, 1000 Genomes); PP3 (multiple in silico prediction tools consistently suggest a deleterious effect on the gene or gene product). Integrating this evidence (PM1 + PM2 + PP3), the variant is classified as likely pathogenic based on ACMG guidelines. Experimental data from this study further substantiate the pathogenicity of the c.773T>G variant located in exon 1 of the ABCD1 gene. This finding broadens the spectrum of known pathogenic mutations in ABCD1 associated with X-ALD and provides crucial information for the molecular diagnosis of affected patients.
METHODS: ABCD1 gene sequencing was performed in the Chinese pedigree. The pathogenicity of identified variants was assessed using computational prediction tools. Subcellular localization studies were conducted, and very-long-chain fatty acid (VLCFA) levels were quantified in patient-derived samples.
RESULTS: Sequencing analysis identified a hemizygous missense variant in the ABCD1 gene (c.773T>G; p.Leu258Arg). In silico pathogenicity prediction using SIFT and PolyPhen-2 algorithms classified the p.Leu258Arg substitution as deleterious. Functional characterization revealed that the p.Leu258Arg variant impairs the peroxisomal membrane localization of the ABCD1 protein. Consistent with the established role of ABCD1 in peroxisomal β-oxidation, individuals harboring this variant exhibited significantly elevated serum levels of VLCFA. Specifically, the C26:0/C22:0 ratio was elevated 2.8-fold compared to control values, confirming impaired VLCFA metabolism.
CONCLUSION: In accordance with the "Standards and Guidelines for the Interpretation of Sequence Variants" established by the American College of Medical Genetics and Genomics (ACMG), we assessed the pathogenicity of the novel ABCD1 gene variant c.773T>G. This variant meets the following ACMG evidence criteria: PM1 (located within a critical functional domain or mutational hotspot known to lack benign variation); PM2 (absent or observed at very low frequency in population databases e.g., gnomAD, EXAC, 1000 Genomes); PP3 (multiple in silico prediction tools consistently suggest a deleterious effect on the gene or gene product). Integrating this evidence (PM1 + PM2 + PP3), the variant is classified as likely pathogenic based on ACMG guidelines. Experimental data from this study further substantiate the pathogenicity of the c.773T>G variant located in exon 1 of the ABCD1 gene. This finding broadens the spectrum of known pathogenic mutations in ABCD1 associated with X-ALD and provides crucial information for the molecular diagnosis of affected patients.