For decades, geneticists have brushed past a class of DNA changes known as synonymous variants, assuming that because they do not alter the protein’s amino acid sequence, they must be harmless. A new study published in the Journal of Translational Medicine upends that assumption for the PROS1 gene, which encodes Protein S, a critical natural anticoagulant. The research, led by Huayang Zhang and Ying Zhao of Zhongshan Hospital, Fudan University, together with Dario Balestra and Francesco Bernardi of the University of Ferrara, shows that so-called silent mutations in PROS1 can sabotage gene expression through several post-transcriptional mechanisms, lowering Protein S levels and predisposing carriers to thrombosis. Just as strikingly, the team demonstrated that engineered RNA molecules can partially correct the damage, opening a path toward variant-specific therapies for inherited thrombophilia.
Protein S is a cofactor for the activated protein C system, one of the body’s principal brakes on blood coagulation. When PROS1 function is impaired, the clotting cascade runs unchecked, and affected individuals face elevated risks of deep vein thrombosis and pulmonary embolism. Genetic testing for Protein S deficiency routinely encounters variants of uncertain significance, or VUS, and synonymous changes are among the most frequently dismissed, typically labeled benign because the protein sequence appears intact. The new study set out to test whether that dismissal is justified, systematically evaluating fourteen synonymous PROS1 variants with an unusually comprehensive experimental toolkit.
The investigators combined computational prediction with laboratory validation. In silico analyses assessed each variant’s likely impact on pre-mRNA splicing, messenger RNA stability, and codon usage, the preference for particular synonymous codons that can influence how efficiently ribosomes translate a transcript. The team then moved to bench experiments, deploying minigene splicing assays to see how each variant altered RNA processing in a controlled cellular setting, measuring mRNA decay rates to quantify transcript stability, and running protein expression and anticoagulant activity assays to determine the downstream functional consequences.
The results were unambiguous: these silent mutations are anything but silent. Six of the fourteen variants, or 42.9 percent, caused aberrant pre-mRNA splicing, meaning the cellular machinery misprocessed the RNA intermediate and produced faulty transcripts. Two variants, 14.3 percent, reduced mRNA stability, hastening the degradation of the PROS1 message before enough Protein S could be made. Another two variants, also 14.3 percent, impaired translational efficiency, leaving ribosomes less able to convert the message into functional protein. In every affected case, the molecular defect cascaded into decreased Protein S expression and diminished anticoagulant activity in the relevant assays.
The clinical significance of these findings was reinforced by data from three additional patients carrying spliceogenic PROS1 variants. Each of these individuals exhibited reduced Protein S levels and thrombotic manifestations that matched the functional defects identified experimentally, providing a genotype-phenotype correlation that links laboratory mechanism to real-world disease. This convergence of molecular and clinical evidence is precisely what variant interpretation guidelines have long demanded but rarely received for synonymous changes.
That convergence had immediate diagnostic consequences. By integrating the multi-layer functional evidence with clinical data, the researchers were able to reclassify several variants under the American College of Medical Genetics and Genomics and Association for Molecular Pathology framework, the standard rubric for assessing pathogenicity. Variants previously parked in the VUS category were moved to likely pathogenic or, in some cases, benign, sharpening the molecular diagnosis of Protein S deficiency and giving clinicians firmer ground for counseling patients and their families about thrombotic risk.
Perhaps the most forward-looking part of the study is its therapeutic proof of concept. Rather than stopping at diagnosis, the team pursued mechanism-guided RNA correction. For selected spliceogenic variants, they engineered modified U1 small nuclear RNAs, components of the spliceosome that can be tailored to recognize mutated splice sites, and antisense U7 snRNAs, which can block aberrant splice sites or redirect the splicing machinery. Delivered into cells, these engineered molecules partially restored normal splicing patterns for the targeted variants, demonstrating that the molecular defects are not only identifiable but potentially correctable.
The implications extend well beyond a single gene. Synonymous variants populate every protein-coding gene in the genome, and growing evidence indicates they can contribute to disease through splicing disruption, mRNA destabilization, altered microRNA binding, and impaired translation. Yet in routine clinical reporting they are still too often waved through as benign. The PROS1 study offers a template for how to interrogate them properly: pair computational screening with minigene assays, mRNA measurements, and protein-level functional readouts, then anchor the findings in patient phenotype data. Applied more broadly, such pipelines could rescue meaningful diagnoses from the VUS backlog that clogs modern genomics.
For patients with inherited thrombophilia, the therapeutic angle is particularly compelling. Current management of Protein S deficiency relies on anticoagulant drugs and vigilance rather than correction of the underlying defect. RNA-based splice correction, already being explored in other genetic diseases, offers a strategy that is variant-specific yet conceptually scalable: once a patient’s spliceogenic variant is defined, a tailored snRNA could in principle be designed to fix it. The partial restoration achieved in this study is an early step, and translating engineered snRNAs from cell culture to safe, effective human therapy will require substantial further development, but the feasibility argument has now been made for PROS1-related thrombosis.
The study also carries a cautionary message for genetic counseling. A synonymous PROS1 variant reported as benign today could, in a family with unexplained thrombosis, be the culprit. As functional evidence accumulates, guidelines will need to keep pace, and laboratories may need to treat synonymous variants near splice junctions or in conserved codon contexts with greater suspicion. What this research makes clear is that the genome’s apparent redundancy conceals layers of regulation, splicing, transcript stability, and translation, that mutation can disturb without changing a single amino acid. In the case of PROS1, listening to those silent signals revealed both hidden causes of a dangerous clotting disorder and a credible route toward fixing them with RNA.
Subject of Research: Functional and clinical characterization of synonymous PROS1 variants causing Protein S deficiency and their RNA-based splicing correction
Article Title: Comprehensive molecular and clinical characterization of synonymous PROS1 variants: from molecular mechanisms to RNA-based splicing correction
Article References: Zhang, H., Su, X., Yu, Q., Pan, B., Ma, D., Francesco, B., Guo, W., Wang, B., Balestra, D., & Zhao, Y. (2026). Comprehensive molecular and clinical characterization of synonymous PROS1 variants: from molecular mechanisms to RNA-based splicing correction. Journal of Translational Medicine. https://doi.org/10.1186/s12967-026-09005-0
Image Credits: AI Generated
DOI: 10.1186/s12967-026-09005-0
Keywords: PROS1, Protein S deficiency, synonymous variants, RNA splicing, thrombophilia, U1 snRNA, U7 snRNA, ACMG/AMP classification, mRNA stability, variant interpretation, RNA therapeutics, minigene assay
