Novel mutations associated with pyruvate kinase deficiency in Brazil

Abstract

BackgroundPyruvate kinase deficiency is a hereditary disease that affects the glycolytic pathway of the red blood cell, causing nonspherocytic hemolytic anemia. The disease is transmitted as an autosomal recessive trait and shows a marked variability in clinical expression. This study reports on the molecular characterization of ten Brazilian pyruvate kinase-deficient patients and the genotype–phenotype correlations.MethodSanger sequencing and in silico analysis were carried out to identify and characterize the genetic mutations. A non-affected group of Brazilian individuals were also screened for the most commonly reported variants (c.1456C>T and c.1529G>A).ResultsTen different variants were identified in the PKLR gene, of which three are reported here for the first time: p.Leu61Gln, p.Ala137Val and p.Ala428Thr. All the three missense variants involve conserved amino acids, providing a rationale for the observed enzyme deficiency. The allelic frequency of c.1456C>T was 0.1% and the 1529G>A variant was not found.ConclusionThis is the first comprehensive report on molecular characterization of pyruvate kinase deficiency from South America. The results allowed us to correlate the severity of the clinical phenotype with the identified variants.

Molecular heterogeneity of pyruvate kinase deficiency

“… 4 , 5 the entire lifespan of erythrocytes. 13 Pathological mutations causing PK deficiency can be localized in any of the protein domains, with major clusters in specific regions, such as the interface between the A and C domains, the A/A′ intersubunit interface, the hydrophobic core of the A domain, and the fructose 1,6 bisphosphate-binding site 6 , 10 , 14 , 15 ( Figure 1C ).…”

The interpretation of rare or novel variants: damaging vs. disease-causing

“…In this issue of the Brazilian Journal of Hematology and Hemotherapy, Svidnicki et al identified variants in the PKLR gene associated with pyruvate kinase deficiency and used the ACMG criteria to evaluate their clinical significance. 6 The study contributes to the molecular characterization of a recessive disorder in a population with a complex genetic background that has not been screened in the same proportion as the American or European populations. The South American population, specifically, the Brazilian population, is underrepresented in most of the genome databases.…”

“…Svidnicki et al identified the R486W PKLR variant in 0.1% of their controls. 6 In the ABraOM consortium database ( http://abraom.ib.usp.br/ ) the same variant has a frequency of 0.32%. The ABraOM is a pioneering initiative attempting to overcome this limitation by providing genetic variability among Brazilians.…”

“…Following the ACMG criteria, Svidnicki et al, 2017 classified three novel variants as of uncertain significance, probably due to the lack of functional or family history data, the main limitations in the process of assessing the pathogenicity of novel variants. 6 In general, the combination of different tools for in silico prediction, well-established criteria to classify variants, a variant allele frequency control from ExAC or GnomAD, familial investigation, and functional data are critical to increase the reliability of sequencing results and to provide evidence for pathogenicity ( Figure 1 ).

Figure 1 Interpretation of novel or rare genetic variants according to the established American College of Medical Genetics and Genomics and Association for Molecular Pathology (ACMG) consensus criteria.

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Pyruvate kinase deficiency: novel mutations and a better understanding of the genotype-to-phenotype correlation in Brazilian patients

“…In this issue of the Brazilian Journal of Hematology and Hemotherapy, Svidnicki et al report on the molecular characterization of ten Brazilian PK-deficient patients and its correlation with the clinical phenotype severity with the identified variants. 8 They also studied a non-affected group of Brazilian individuals screened for the most commonly reported variants. Ten different variants of the PK LR gene were identified, of which three are reported here for the first time: p.Leu61Gln, p.Ala137Val and p.Ala428Thr.…”