A Unique Mechanism of a Novel Synonymous PHEX Variant Causing X-Linked Hypophosphatemia

J Clin Endocrinol Metab. 2022 Sep 28;107(10):2883-2891. doi: 10.1210/clinem/dgac435.

PMID: 35896147

Kheloud M Alhamoudi, Balgees Alghamdi, Meshael Alswailem

Highlights: This article presents a family with X-linked hypophosphatemia (XLH) due to a novel synonymous PHEX variant with a unique mechanism.

Abstract:

Context: Synonymous mutations are usually nonpathogenic.

Objective: Here, a case of X-linked hypophosphatemia (XLH) is presented in a family caused by a novel synonymous PHEX variant with a unique mechanism.

Methods: A family of four was studied, including a mother, son, and two daughters, who were all impacted by XLH. Leucocytes from the periphery were used to harvest genomic DNA. The proband's (the son's) underlying genetic variant was found using whole exome sequencing (WES). This variant was verified in the proband and his family members using Sanger sequencing. The impact of this variant on the PHEX structure and function was discovered by RT-PCR and cDNA sequencing.

Results: The PHEX gene (c.1701A>C) synonymous variant was found in all affected family members. The first nucleotide of exon 17 is changed from adenine to cytosine in this variant. By interfering with the splicing of exons 16 and 17, it was demonstrated via RT-PCR that the proband's PHEX transcript was shorter than that of the normal control. Exon 17 was completely skipped during the cDNA's Sanger sequencing, and exons 16 and 18 were directly spliced in their place. This resulted in a frameshift and the addition of a new stop codon in the following codon (codon 568), which ultimately caused PHEX's final 183 amino acids to be truncated and lost.

Conclusion: This unique variant demonstrates an uncommon method by which a synonymous exonic mutation may result in a complicated series of changes in the gene's transcription and translation and lead to illness.

Keywords: FGF23, PHEX, X-linked hypophosphatemia, splicing site, synonymous variant, whole exome sequencing, zinc-binding site