OC 08.1 - The rare Ser569Ser (c.1707C>T) PROS1 variant induces a frameshift due to a splicing defect and is enriched in patients with venous thrombosis

Saturday, June 22, 2024

13:00 – 13:15 ICT

Room: 211 A-D

Presenting Author(s)

Pierre Morange, MD, PhD

Aix-Marseille University, France

Co-Author(s)

OS

Omar Soukarieh

Post Doctoral Fellow
INSERM U1034, Pessac
Bordeaux, Aquitaine, France
NS

Noémie Saut

Research Assistant
C2VN, INRAE, INSERM Aix-Marseille University, Marseille, France,
Marseille, Provence-Alpes-Cote d'Azur, France
SL

Sylvie Labrouche-Colomer

PhD
Laboratoire d’Hémostase moléculaire, Groupe hospitalier Pellegrin, CHU de Bordeaux, 33000 Bordeaux, France
Bordeaux, Aquitaine, France
JD

Jean-François Deleuze

Director
CNRGH, CEA, France
Evry, Ile-de-France, France
Pierre Suchon

Clinial Research Investigator
C2VN, INRAE, INSERM Aix-Marseille University, Marseille, France,
Marseille, Provence-Alpes-Cote d'Azur, France
David-Alexandre Trégouët

Senior Investigator
Bordeaux Population Health research Center, Inserm U1219, Bordeaux University
Bordeaux, Aquitaine, France

Background: A small proportion of the genetic determinants of venous thrombosis (VT) have been identified so far.

Aims: To identify and characterize the molecular defect responsible for unexplained thrombophilia in a man with unprovoked proximal VT at 26 years old and strong family history of VT and normal biological thrombophilia screening including a free protein S (PS) concentration of 64% in plasma.

Methods: Whole genome sequencing (WGS) was performed. Various bioinformatics tools were used to prioritize candidates, including several recent splicing-dedicated methods. Minigene-based splicing assay were performed to complement in silico predictions. Candidate variants were genotyped in an independent sample of 493 VT patients.

Results: WGS identified as best plausible culprit the rare synonymous Ser569Ser (c.1707C>T) variant in PROS1 gene, coding for the PS. This variant is located in exon 14, and is classified as variant of unknown significance in ClinVar. It is predicted to create a new acceptor splice site within exon 14. A minigene splicing assay was performed and confirmed the skipping of the first 89 nucleotides of exon 14, resulting from the use of the predicted new acceptor site. The associated splicing defect leads to a frameshift and the generation of a premature stop codon, suggesting the degradation of the transcripts by the nonsense mediated decay. Moreover, 2 patients carrying the Ser569Ser variant were identified out of 493 unrelated patients with unprovoked VT. Free PS concentrations in plasma were 51% for both patients.

Conclusion(s): The PROS1 Ser569Ser is a strong candidate genetic factor for unprovoked VT. The ongoing validation of the observed splicing defect in patients’ RNA will provide better understanding of the link between this variant and VT.