Biallelic Variant in the AGXT Gene in a Family Segregating Primary Hyperoxaluria; Accurate Genetic Diagnosis and Carrier Detection

Abstract

Aim: Autosomal recessive primary hyperoxalurias (PH) are genetic disorders characterised by elevated oxalate production. Mutations in genes involved in glycoxylate metabolism are the underlying cause of PH. Type 1 PH (PH1) results in malfunctioning of alanine-glyoxylate aminotransferase enzymes of liver due to a change in the genetic sequence of alanine-glyoxylate aminotransferase (AGXT) gene. We encountered a large family segregating genetic disease of high oxalate kidney stones. A genetic analysis was carried out with the aim to identify underlying genetic defect.

Methods: A large family with multiple affected individuals was recruited for this study. An extensive clinical evaluation, followed by genetic analysis, was carried out. Due to the heterogeneous nature of the disease, two members of the family having disease symptoms were subjected to whole exome sequencing (WES). Variants were annotated, filtered, and prioritised using various bioinformatic tools to detect disease associated genetic defects.

Results: Unbiased and hypothesis-free WES data analysis was performed. Raw reads (fastq files) were mapped to the reference genome and duplicates were removed. Variants were annotated, filtered, and prioritised. A low-frequency missense variant (c. 1049G>A) in the AGXT gene was considered the candidate variant. This variant replaces the highly conserved glycine amino acid with aspartate (p.Gly350Asp). The variant is destabilising for protein-protein interaction based on predicted change in binding free energy (ΔΔG). All members having disease phenotype were found homozygous to the mutation. Both parents and unaffected individuals in a family are heterozygous for the variant.

Conclusion: Identification of pathogenic variant in the AGXT gene, in this family, provides genotype-phenotype correlation and permits accurate clinical diagnosis as well as carrier detection. Moreover, this variant extends the AGXT mutation spectrum in a different population and highlights the clinical significance and diagnostic relevance of the variant.

Keywords: alanine‐glyoxylate transaminase; clinical relevance; computational biology; exome sequencing; mutation.