A Novel Missense Variant Associated with A Splicing Defect in A Myopathic Form of PGK1 Deficiency in The Spanish Population

Abstract

Phosphoglycerate kinase (PGK)1 deficiency is an X-linked inherited disease associated with different clinical presentations, sometimes as myopathic affectation without hemolytic anemia. We present a 40-year-old male with a mild psychomotor delay and mild mental retardation, who developed progressive exercise intolerance, cramps and sporadic episodes of rhabdomyolysis but no hematological features. A genetic study was carried out by a next-generation sequencing (NGS) panel of 32 genes associated with inherited metabolic myopathies. We identified a missense variant in the PGK1 gene c.1114G > A (p.Gly372Ser) located in the last nucleotide of exon 9. cDNA studies demonstrated abnormalities in mRNA splicing because this change abolishes the exon 9 donor site. This novel variant is the first variant associated with a myopathic form of PGK1 deficiency in the Spanish population.

Keywords: PGK1 deficiency; abnormalities in mRNA splicing; missense variant; myopathic form; phosphoglycerate kinase 1 gene (PGK1).

Figure 1

(A) Evolutionary conservation of the G372 residue among different species. Asterisk, fully conserved residue; colon, conservative replacement; period, semi-conservative replacement. (B) DNA sequence chromatograms. The picture shows the sequencing results of the patient and his parents from the genomic DNA variant c.1114G > A (p.G372S) in the PGK1 gene. Hemizygous index case c.1114A (1b), heterozygous mother c.1114GA (2b) and wild type father (3b).

Figure 2

Family pedigree illustrating the patient’s family, showing that the patient mother is a carrier of the variant. The four sisters of the patient’s mother and the patient’s sister have not been analyzed for their carrier status.

Figure 3

Analysis of the PGK1 patient’s blood cDNA. (A). Electrophoresis on 1% agarose gel. Lane 1: Index case showing a transcript of normal size (b band), one higher molecular weight cDNA species (a band), and an apparently more abundant transcript of lower molecular weight (c band); Lane 2: Healthy control showing a transcript of normal size (b band). (B). Sanger Sequencing of the gel purified amplicons. (1a): Sequence of patient’s a band showing the retention of intron 9; (1b): Sequence of the patient’s b band displaying the junction of exons 9 and 10, and the variant c.1114G > A (indicated by an arrow). Healthy control revealed the same pattern for b band (not shown). The hemizygous c.1114G > A variant was detected in the patient’s sequence of a transcript of normal size (1b); (1c): Sequence of patient’s c band showing the skipping of exon 9 in the cDNA.

Figure 4

Schematic representation of the described mutations in the PGK1 gene, represented by separate mutations associated with hemolytic anemia and mutations present in non-hemolytic forms. (Black star: mutations affecting splicing. Grey star: mutation in which it has been ruled out that the splicing is altered).