Identification of novel compound heterozygous PFKM variants in a patient with chronic haemolytic anaemia: genotype–phenotype correlation and structural insights and Mutation update

Background Phosphofructokinase (PFK) is a key rate-limiting enzyme of glycolysis essential for cellular energy metabolism, particularly in erythrocytes that rely entirely on glycolysis for ATP production. Pathogenic variants in the PFKM gene cause glycogen storage disease type VII (Tarui disease), a rare autosomal recessive disorder characterised by impaired glycolysis, resulting in exercise intolerance, myopathy, and haemolytic anaemia. The clinical spectrum is highly heterogeneous, ranging from isolated muscle involvement to predominant haematological manifestations. Despite numerous variants reported globally, the molecular spectrum and genotype–phenotype correlations remain poorly defined in several populations, including India. Methods Haematological, biochemical, and red cell enzyme analyses were performed in a patient suspected of haemolytic anaemia. Whole-exome sequencing with variant annotation and ACMG classification was conducted, and findings were validated by Sanger sequencing. Structural impact of variants was assessed using in silico modeling (PDB: 3O8L) in PyMOL. Results A patient with chronic haemolytic anaemia showed biochemical evidence of haemolysis and hepatobiliary involvement. Whole-exome sequencing identified two novel compound heterozygous PFKM variants (p.Arg184Trp and p.Leu324Pro), predicted to be deleterious and affecting conserved residues. Structural analysis suggested disruption of the ADP-binding region and protein stability, supporting their potential pathogenic role. Conclusion This study expands the mutational spectrum of PFKM and highlights its variable clinical presentation, with predominant haemolytic anaemia. Early molecular diagnosis combined with structural analysis is crucial for accurate diagnosis, understanding disease mechanisms, and guiding management.