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3972 Clinical Consequences of Rare Germline Variation in Genes Associated with Coagulation across 451,958 Individuals

Program: Oral and Poster Abstracts
Session: 321. Coagulation and Fibrinolysis: Basic and Translational: Poster III
Hematology Disease Topics & Pathways:
Research, Bleeding and Clotting, bleeding disorders, Translational Research, bioinformatics, genomics, thromboembolism, Diseases, thrombotic disorders, Biological Processes, Technology and Procedures, omics technologies
Monday, December 11, 2023, 6:00 PM-8:00 PM

Justine Ryu, MD1,2, Amelia K Haj, MD, PhD2,3,4, Satoshi Koyama, MD2*, Sean J. Jurgens, MD MSc2,5,6*, Simone Sanna-Cherchi, MD7*, Patrick Ellinor, MD, PhD2,4,6* and Pavan K Bendapudi, MD4,8,9,10,11

1Section of Hematology, Yale University School of Medicine, New Haven, CT
2The Broad Institute of MIT and Harvard, Cambridge, MA
3Department of Pathology, Massachusetts General Hospital, Cambridge, MA
4Harvard Medical School, Boston, MA
5Department of Experimental Cardiology, University of Amsterdam, Amsterdam, Netherlands
6Massachusetts General Hospital, Boston, MA
7Division of Nephrology, Columbia University Irving Medical School, New York, NY
8Division of Thrombosis and Hemostasis, Beth Israel Deaconess Medical Center, Boston, MA
9Blood Transfusion Service, Department of Pathology, Massachusetts General Hospital, Boston, MA
10Division of Hematology, Department of Medicine, Massachusetts General Hospital, Cambridge, MA
11Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, Cambridge, MA


Despite deep biological insights over the preceding decades, our ability to assess for inherited hypercoagulable states remains limited. In light of these challenges and the increasing relevance of precision medicine and next-generation sequencing (NGS) to clinical practice, the identification of rare germline variants in coagulation-focused NGS panels is increasingly becoming accepted practice. However, the discovery of variants of unknown significance (VUS) remains a common clinical conundrum in molecular testing, particularly because evidence for the thrombosis risk associated with many genes derives from small, uncontrolled studies, case reports, and pedigree analysis. Large-scale evaluation of the clinical consequences associated with loss of function in individual coagulation-related genes would contribute to the clinical assessment of patients presenting with heterozygous VUS in poorly characterized genes.


Determine the risk of four thrombosis phenotypes associated with rare, germline loss-of-function variants in a major clinical coagulation-focused NGS panel.


The UK Biobank (UKBB) contains paired clinical and whole exome sequencing data for over 450,000 participants. We identified rare (minor allele frequency <0.1%) germline variants that were predicted in silico to alter protein activity (functional impact score ≥0.8) within the 54 evaluable genes of the Yale NGS coagulation panel. For each gene, parallel multivariable Firth’s logistic regression models were generated to assess the association between rare qualifying variants and four thrombotic phenotypes as well as coagulopathic bleeding in a gene-level collapsing analysis (N=270 independent models). We adjusted for age, sex, ancestry, and sequencing batch. Phenotypes of interest included venous thromboembolism (VTE), myocardial infarction (MI), stroke (CVA), peripheral artery disease (PAD), and coagulopathic bleeding. The Bonferroni corrected p-value for each phenotype was 0.001. We validated functional impact score predictions in seven secreted proteins measured in a subset of 47,923 UKBB participants who underwent plasma proteomic assessment (Olink Explore 1536 panel).


A total of 451,958 individuals in the UKBB with whole exome sequencing data were evaluated. Among the 54 genes in the Yale NGS coagulation panel, there were 18,975 qualifying variants (98.4% heterozygous). Function-altering variants in 4 of 54 genes were associated with a statistically significant increased risk of thrombosis after adjusting for multiple comparisons: PROC (OR = 5.7, 95% CI: 3.2 – 9.6, p = 1.6x10-7), SERPINC1 (OR = 5.0, 95% CI: 2.7 – 8.7, p = 4.0x10-6), PROS1 (OR = 3.2, 95% CI: 2.0 – 4.8, p = 6.0x10-6), and STAB2 (OR = 1.4, 95% CI: 1.2 – 1.7, p = 5.3x10-4) (Figure 1). Nominal significance was achieved for 7 genes in the VTE phenotype, 1 gene in CVA, 3 genes in MI, 5 genes in PAD, and 0 genes in coagulopathic bleeding. Variants in a total of 37 genes did not appear to be significantly associated with any of the evaluated phenotypes. To assess the reliability of variant functional impact scores derived in silico, plasma levels for 13 of the 53 coagulation genes were analyzed. Of these, 8 were identified as secreted proteins amenable to assessment by plasma levels, including ADAMTS13 (ADAMTS13), factor IX (F9), factor VII (F7), tissue plasminogen activator (PLAT), urokinase (PLAU), protein C (PROC), plasminogen activator inhibitor 1 (SERPINE1), and von Willebrand factor (VWF). For these proteins, average plasma levels consistently demonstrated a negative correlation with functional impact score (Pearson r = -0.98, P=0.0009), indicating that our in silico assessments in this context are broadly reliable (Figure 2).


Within the commonly encountered clinical context of heterozygous loss of function, most genes contained in coagulation-focused NGS panels likely have fairly weak effects on disease risk that are limited to venous thrombosis. However, our findings do not rule out the possibility of more profound effects from homozygous or compound heterozygous loss of function in these same genes. By defining the clinical consequence of heterozygous loss of function in specific coagulation-related genes across a large population, our findings may help inform the interpretation of molecular testing results in which patients are found to have a VUS.

Disclosures: Ellinor: Novartis: Consultancy; Bayer AG: Consultancy, Research Funding. Bendapudi: Alexion Pharmaceuticals: Consultancy; Takeda Pharmaceuticals: Consultancy.

*signifies non-member of ASH