Only a small percentage of individuals with low plasma levels of protein S have a mutation in the coding region of PROS1, the gene encoding a key circulating anti-coagulant factor. Additionally, a complete heterozygous protein S deficiency in which one copy of the PROS1 gene is nonfunctional is both rarer and more strongly linked to venous thrombosis than previously thought. These results, from a population-based study using U.S.- and U.K.-based databases, were published in JAMA.
In the current study, Pavan K. (Tem) Bendapudi, MD, assistant professor of medicine at Harvard Medical School in Boston, and his colleagues assessed the prevalence of protein S deficiency and evaluated the risk associated with protein S deficiency across multiple thrombosis phenotypes. The team analyzed data from two longitudinal population cohorts: the U.K. Biobank, which contains data on 426,436 individuals, 95.6% of whom are of European descent, and the U.S. National Institutes of Health (NIH) All of Us biorepository of 204,006 individuals.
All U.K. Biobank participants underwent whole-exome sequencing, and 44,431 had protein S levels measured by high-throughput plasma proteomics. Participants in NIH’s All of Us underwent germline whole-genome sequencing. Both cohorts included individual-level data on demographics, laboratory measurements, and clinical outcomes. The authors analyzed the sequencing data for rare germline genetic variants in PROS1.
Carriers with a likely deleterious PROS1 missense variant were significantly more likely to develop venous thromboembolism (VTE) after adjusting for age, sex, and ancestry (odds ratio [OR] = 1.98; p=1.95 × 10−7). Those who carried a complete loss-of-function variant in PROS1 (resulting in truncation, frameshift, or disruption of an essential splice site) were even more likely to develop VTE (OR=14.01; p=9.1 × 10-11). The investigators found that only 9.1% of participants who met a clinically defined threshold for protein S deficiency (total plasma protein S <60%) had a deleterious mutation in PROS1, even after removing individuals who were on oral contraceptives or warfarin.
“That only 10% or so of individuals with low total protein S plasma levels have a mutation within the coding region of PROS1 is very surprising, because most individuals with protein S deficiency are assumed to have an inherited cause,” Dr. Bendapudi said. “We also found that heterozygous loss of PROS1 greatly increases the risk of venous thrombosis in the general population, which challenges the common teaching in hematology that inherited protein S deficiency only weakly contributes to thrombosis. Our data suggest that the risk for venous thrombosis in these individuals approaches that seen in type I antithrombin deficiency, which is typically considered to be the most clinically severe of the inherited thrombosis disorders.”
The prevalence of PROS1 mutations that lead to protein S deficiency has been unclear due to a lack of large studies with data linking genetic information and outcomes at the individual level. Researchers found that the prevalence of heterozygous complete loss-of-function mutations in PROS1 is lower than previously thought (about 1:10,000 individuals) but causes a highly penetrant phenotype. By comparison, missense mutations in a PROS1 allele that result in less-than-complete loss of protein S production were more common (about 1:500 individuals) and associated with a smaller increase in thrombosis risk.
However, unlike the strong association between PROS1 loss-of-function variants and VTE, the authors did not see a significant association between protein S deficiency and the risk of arterial thrombosis conditions, such as myocardial infarction, peripheral artery disease, and non-cardioembolic ischemic stroke. An analysis of the U.S. All of Us cohort showed similar findings across all thrombosis types.
“It has previously been controversial as to whether inherited protein S deficiency predisposed people to arterial thrombosis, and we were able to use an extremely large state-of-the-art dataset to address this issue,” Dr. Bendapudi noted.
Additional research is needed on the link between PROS1 mutational status, protein S levels, and VTE prior to changing recommendations for clinical care. Currently, clinicians screen for protein S deficiency using blood tests that measure the level and activity of protein S in the blood. “Still, our data suggest that assays for total plasma protein S are probably more useful than previously recognized and do a fairly good job of identifying patients at higher risk for a first venous thrombosis event. We propose sequencing of the PROS1 gene in individuals found to have low total protein S levels in order to identify patients who are heterozygous for complete loss-of-function mutations in PROS1. These mutation carriers may warrant long-term anticoagulation or other preventive measures after a first VTE event to modulate their exceptionally high risk of thrombosis,” Dr. Bendapudi said.
Dr. Bendapudi and colleagues are now following up on the work to identify other potential genes beyond PROS1 that are involved in regulating plasma protein S levels and may affect VTE risk.
Any conflicts of interest declared by the authors can found in the original article.
Reference
Chaudhry SA, Haj AK, Ryu J, et al. Population-scale studies of protein S abnormalities and thrombosis [published online ahead of print, 2025 March 3]. JAMA. doi: 10.1001/jama.2025.0155.
Perspectives
Were the study findings surprising in any way?
To date, current understanding of thrombosis risk in protein S deficiency is limited by small, nondefinitive studies. The authors of this study analyzed two population-scale databases of individuals who were protein S deficient, one from the U.K. Biobank and one from the U.S. NIH All of Us biorepository. They performed genomics and proteomics on more than 600,000 individuals with protein S deficiency and analyzed the findings with individual clinical and laboratory data. This provided sufficient power to identify high-risk genes and derive estimates of arterial and venous thrombosis.
The most striking finding is that thrombosis risk in protein S deficiency is not necessarily mild. This has not been previously established. Those with disruptive mutations in the protein S PROS1 gene, specifically nonsense, frameshift, or splice site variants, were found to have a very high risk of thrombosis with an OR of 14.01.
Those with protein S deficiency due to acquired or environmental causes and no PROS1 variant are more likely than those with the PROS1 variant to develop venous thrombosis or arterial thrombosis.
Do the results have actionable implications for this population?
Those with protein S deficiency, defined as low protein S antigen (free or total), or in whom protein S testing is indicated (e.g., members of an affected kindred), should have their PROS1 gene sequenced. That is important because detection of PROS1 variants indicates a high risk of thrombosis. The clinical relevance of having a high risk of thrombosis may suggest the need for longer-term anticoagulation for acute thrombosis or the need for longer-term thromboprophylaxis, for example, for those with a nonsurgical major transient risk or hormonal risk, in the antepartum or postpartum period, or for ambulatory cancer management.
Are there any limitations of the study or further questions that need to be explored?
These findings regarding thrombosis risk in protein S deficiency will require critical review by the American Hematology Society’s VTE guidelines experts to update anticoagulation recommendations.
Margaret V. Ragni, MD, MPH
Department of Medicine, Division of Classical Hematology
University of Pittsburgh
COI: Dr. Ragni reports research support, consultancy, advisory board, and/or speaking activities for Alnylam, BeBio, BioMarin, Hemab Therapeutics, Sanofi, Spark Therapeutics, Takeda Pharmaceuticals, Institute for Economic Review, Foundation for Women and Girls with Bleeding Disorders, and Hemostasis & Thrombosis Research Society. She also serves as associate editor for Blood Advances, a journal of the American Society of Hematology.
