RDDC Tool Precisely Predicts Pathogenic Splicing from a TCF4 3'UTR Variant
In complex genetic diagnostics, researchers often face a dead end when Chromosomal Microarray Analysis (CMA) and Whole Exome Sequencing (WES) return negative. Variants in non-coding regions, especially the 3'UTR, are a new frontier, but their functional consequences are notoriously difficult to predict. A recent study on Pitt-Hopkins syndrome (PTHS) perfectly demonstrates the power of combining Whole Genome Sequencing (WGS) with advanced bioinformatics. In this study, the RDDC RNA Splicer algorithm provided critical, actionable predictions that were ultimately confirmed by Sanger sequencing, setting a new precedent for solving WES-negative cases.
The Clinical Challenge: A WES-Negative Neurodevelopmental Disorder
The challenge began with a 4-year-old Chinese boy presenting with global developmental delay, inability to walk independently, no spontaneous speech, and typical PTHS facial features. However, all standard genetic tests, including WES, had failed to find a pathogenic cause. This strongly suggested the culprit variant was lurking outside the exome.
WGS Uncovers a 3'UTR "Variant of Uncertain Significance"
The research team escalated to WGS and identified a de novo heterozygous variant in the 3'UTR of the TCF4 gene (near the stop codon): c.*1A>G. This variant was not reported in gnomAD or other major databases. Located in a non-coding region, its pathogenicity was not intuitive, making it a classic "Variant of Uncertain Significance" (VUS).
RDDC's Precision: From VUS to a Clear Mechanism
How could the team determine if this 3'UTR variant was pathogenic? They employed several splicing prediction tools, including RDDC. While other tools suggested a potential change in splicing, the RDDC RNA Splicer algorithm provided three specific, testable predictions for abnormal splicing patterns:
- Activation of a new splice donor site, resulting in an 8 bp deletion;
- Skipping of exon 19 (a 141 bp deletion);
- Retention of intron 10 (a 190 bp insertion).
RDDC's predictions were not just probabilities; they were concrete hypotheses that provided a clear roadmap for wet-lab validation.
Sanger Sequencing Confirms RDDC's Prediction
Following this in silico lead, the team performed functional validation. PCR and Sanger sequencing of the patient's mRNA revealed the presence of an 8 bp deletion. This finding was a perfect match for RDDC's first prediction. This deletion caused a loss of the stop codon and a translational frameshift, definitively proving the pathogenicity of the c.*1A>G variant.
Case Implications: An Essential AI Tool in the WGS Era
This case clearly demonstrates that for WES-negative disorders, WGS is the key to finding non-coding variants. However, translating WGS data into a definitive diagnosis requires powerful AI bioinformatics tools like the RDDC RNA Splicer. RDDC's predictive accuracy successfully bridged the gap from a 3'UTR VUS to a validated pathogenic splicing variant, proving it is an indispensable asset for researchers tackling the functional study of non-coding variants.
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
Wang S, Li J, Li D, et al. A novel variant in the 3′ UTR of the TCF4 gene likely causes Pitt-Hopkins syndrome: a case report. Journal of Genetics and Genomics. 2024 Feb;51(2):162-165.
Article Link: https://pubmed.ncbi.nlm.nih.gov/39375747/
