Classic Galactosemia: Clinical and Computational Characterization of a Novel GALT Missense Variant (p.A303D) and a Literature Review

Abstract

Classic galactosemia is an autosomal recessive inherited liver disorder of carbohydrate metabolism caused by deficient activity of galactose-1-phosphate uridylyltransferase (GALT). While a galactose-restricted diet is lifesaving, most patients still develop long-term complications. In this study, we report on a two-week-old female patient who is a compound heterozygote for a known pathogenic variant (p.K285N) and a novel missense variant (p.A303D) in the GALT gene. Segregation analysis showed that the patient inherited the p.K285N pathogenic variant from her father and the p.A303D variant from her mother. A bioinformatics analysis to predict the impact of the p.A303D missense variant on the structure and stability of the GALT protein revealed that it may be pathogenic. Based on this finding, we performed a literature review of all GALT missense variants identified in homozygous and compound heterozygous galactosemia patients carrying the p.K285N pathogenic variant to explore their molecular effects on the clinical phenotype of the disease. Our analysis revealed that these missense variants are responsible for a wide range of molecular defects. This study expands the clinical and mutational spectrum in classic galactosemia and reinforces the importance of understanding the molecular consequences of genetic variants to incorporate genetic analysis into clinical care.

Keywords: GALT; classic galactosemia; novel missense variant.

Figure 1

(A) Pedigree of the family involved in this study. Squares indicate men and circles indicate women. The arrow indicates the index case. Black-filled symbols denote individuals with galactosemia, and unfilled symbols indicate unaffected individuals. The vertical bars represent the GALT gene alleles segregating with the disease. (B) Sequencing electropherograms of genomic DNA from the index patient and her parents for all variants detected in the GALT gene.

Figure 2

In silico analysis of GALT A303D variant. (A,B) Missense 3D analysis. Spacefill (A) and cartoon (B) structures of wild-type (wt) GALT (left) and GALT A303D variant (right). The GALT PDB entry considered for the analysis is 5in3. The wt residue Ala is indicated with a blue circle (A) or in blue (B), while the mutant residue Asp is indicated in red. (C) Results of the in silico prediction analysis of the structural and functional impact of the A303D substitution using the indicated computational tools.

Figure 3

Graphical representation of GALT missense variants. (A) Lollipop graph of GALT protein variants. Distribution of GALT missense variants reported as homozygous and compound heterozygous with the c.855G>T (p.K285N) variant in galactosemic patients with clinical information identified in our literature meta-analysis and the present study. Vertical color bars in the amino acid sequence indicate functional sites: zinc-binding sites (brown), Glc-1-P (Glucose-1-phosphate) binding sites (blue), and active site (red). The galactosemia phenotypes associated with the missense variants are also reported: classic galactosemia (red), clinical variant galactosemia (orange), and phenotype not reported (gray). The scale bar on the left indicates the number of patients carrying each GALT missense variant. (B) Schematic representation of GALT coding sequence (NM_000155.4) and distribution of GALT missense variants.