Investigating the structural impacts of a novel missense variant identified with whole exome sequencing in an Egyptian patient with propionic acidemia

Abstract

Propionic Acidemia (PA) is an inborn error of metabolism caused by variants in the PCCA or PCCB genes, leading to mitochondrial accumulation of propionyl-CoA and its by-products. Here, we report a 2 year-old Egyptian boy with PA who was born to consanguineous parents. Biochemical analysis was performed using tandem mass spectrometry (MS/MS) on the patient's dried blood spots (DBS) followed by urine examination of amino acids using gas chromatography/mass spectrometry (GC/MS). Molecular genetic analysis was carried out using whole-exome sequencing (WES). The PCCA gene sequencing revealed a novel homozygous missense variant affecting the locus (chr13:100962160) of exon 16 of the PCCA gene, resulting in the substitution of the amino acid arginine with proline at site 476 (p.Arg476Pro). Computational analysis revealed that the novel variant might be pathogenic and attributed to decrease the stability and also has an effect on the biotin carboxylase c-terminal domain of the propionyl carboxylase enzyme. The physicochemical properties analysis using NCBI amino acid explorer study revealed restrictions in the side chain and loss of hydrogen bonds due to the variant. On the structural level, the loss of beta-sheet was observed due to the variant proline, which has further led to the loss of surrounding interactions. This loss of beta-sheet and the surrounding interactions might serve the purpose of the structural stability changes. The current study demonstrates that a combination of whole-exome sequencing (WES) and computational analysis are potent tools for validation of diagnosis and classification of disease-causing variants.

Keywords: Computational analysis; Genotype-phenotype correlation; Next-generation sequencing; PCCA gene; Propionic acidemia (PA).

Fig. 1

Family Pedigree, demonstrating that the parents of the proband were heterozygous for the p.Arg476Pro variant.

Fig. 2

Ramachandran plot validation of the modeled PCCA 3D protein structure. The plot reveals that the number of residues in the favored region was 89.0%, the number of residues in the allowed region was 8.4%, and the number of residues in the outlier region was 2.6%.

Fig. 3

Computational modeling to predict the impact of novel variant on PCCA protein. The PCCA protein with novel variant p.Arg476Pro (Green) superimposed with the native PCCA (Red) visualized by the Discovery Studio visualizer software. The enlarged image shows the loss of the beta-sheet due to the variant p.Arg476Pro.

Fig. 4

Change in the interacting amino acids between the native arginine and variant proline at the 476th position of PCCA protein. (A) PCCA with native arginine (B) PCCA with variant proline.