Introduction
In genetic diagnostics, "synonymous variants" are often dismissed as "benign" or "VUS" because they do not change the amino acid. This can lead to a diagnostic dead end. However, a recent case report on aplasia of the urogenital system perfectly illustrates the potential pathogenicity of these "silent" variants and highlights the critical value of the RDDC bioinformatics tool in unmasking their mechanism. In this study, RDDC precisely predicted that a GREB1L synonymous variant would cause a 6 bp deletion, a prediction that was subsequently validated by a minigene assay.
The Clinical Challenge: A "Silent" Variant of Uncertain Significance
The challenge involved a 7-year-old female patient presenting with aplasia of the right kidney, uterus, and ovaries. Whole Exome Sequencing (WES) identified a novel de novo synonymous variant in the GREB1L gene: c.4731C>T (p.G1577=).
Because this variant is "synonymous" at the protein-coding level, it would be easily overlooked in a standard analysis pipeline. The research team had to answer the critical question: Is this seemingly harmless variant the true cause of the patient's severe phenotype?
RDDC's Precise Prediction: Unmasking a 6 bp Deletion
To investigate the variant's function, the team used splicing prediction tools, including RDDC and SpliceAI. SpliceAI suggested the variant could create a new splice donor site (Δscore=0.92). The RDDC tool went a step further, providing a specific molecular consequence for this event: it predicted the variant would lead to a 6 bp deletion (c.4730_4735del).
This prediction transformed an abstract C>T synonymous variant into a concrete, testable "6 bp deletion" event.
Perfect Validation by Minigene Assay
Based on RDDC's clear prediction, the team performed a minigene assay. The results were compelling: compared to the wild-type, the cDNA from the mutant c.4731C>T variant was indeed missing exactly 6 base pairs.
This experimental result was in perfect agreement with the RDDC prediction. This 6 bp deletion (p.Val1578_Gly1579del), though small, was shown to alter the protein's secondary and tertiary structure, thus confirming its pathogenicity. The closed loop of in silico prediction and in vitro validation definitively proved the pathogenicity of this "synonymous" variant.
Case Implications
This case powerfully demonstrates that synonymous variants must not be ignored in WES/WGS analysis. Advanced splicing prediction tools like RDDC are essential for researchers. It accurately predicts the hidden splicing errors behind "silent" variants, providing a clear blueprint for functional experiments and serving as a powerful engine for linking genotype to phenotype.
Content Source and Disclaimer
This article is a compilation and interpretation of the scientific study cited below, intended to highlight the application of RDDC bioinformatics tools. All research data and conclusions belong to the original authors and publication.
Original Article:
Han Y, Zhang Y, Xiao J, et al. A novel de novo synonymous variant in GREB1L impacts the mRNA splicing associated with aplasia of the urogenital system. Molecular Genetics & Genomic Medicine. 2023 Sep;11(9):e2226.
Article Link: https://pubmed.ncbi.nlm.nih.gov/39091162/
