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αIIbβ3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia

Buitrago, Lorena; Rendon, Augusto; Liang, Yupu; Simeoni, Ilenia; Negri, Ana; ThromboGenomics Consortium; Filizola, Marta; Ouwehand, Willem H.; Coller, Barry S.

Authors

Lorena Buitrago

Augusto Rendon

Yupu Liang

Ilenia Simeoni

Ana Negri

Marta Filizola

Willem H. Ouwehand

Barry S. Coller



Abstract

Next-generation sequencing is transforming our understanding of human genetic variation but assessing the functional impact of novel variants presents challenges. We analyzed missense variants in the integrin αIIbβ3 receptor subunit genes ITGA2B and ITGB3 identified by whole-exome or -genome sequencing in the ThromboGenomics project, comprising ∼32,000 alleles from 16,108 individuals. We analyzed the results in comparison with 111 missense variants in these genes previously reported as being associated with Glanzmann thrombasthenia (GT), 20 associated with alloimmune thrombocytopenia, and 5 associated with aniso/macrothrombocytopenia. We identified 114 novel missense variants in ITGA2B (affecting ∼11% of the amino acids) and 68 novel missense variants in ITGB3 (affecting ∼9% of the amino acids). Of the variants, 96% had minor allele frequencies (MAF) < 0.1%, indicating their rarity. Based on sequence conservation, MAF, and location on a complete model of αIIbβ3, we selected three novel variants that affect amino acids previously associated with GT for expression in HEK293 cells. αIIb P176H and β3 C547G severely reduced αIIbβ3 expression, whereas αIIb P943A partially reduced αIIbβ3 expression and had no effect on fibrinogen binding. We used receiver operating characteristic curves of combined annotation-dependent depletion, Polyphen 2-HDIV, and sorting intolerant from tolerant to estimate the percentage of novel variants likely to be deleterious. At optimal cut-off values, which had 69–98% sensitivity in detecting GT mutations, between 27% and 71% of the novel αIIb or β3 missense variants were predicted to be deleterious. Our data have implications for understanding the evolutionary pressure on αIIbβ3 and highlight the challenges in predicting the clinical significance of novel missense variants.

Journal Article Type Article
Publication Date Apr 14, 2015
Journal Proceedings of the National Academy of Sciences
Print ISSN 0027-8424
Electronic ISSN 1091-6490
Publisher National Academy of Sciences
Peer Reviewed Peer Reviewed
Volume 112
Issue 15
Pages E1898-E1907
APA6 Citation Buitrago, L., Rendon, A., Liang, Y., Simeoni, I., Negri, A., ThromboGenomics Consortium, , …Coller, B. S. (2015). αIIbβ3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia. Proceedings of the National Academy of Sciences of the United States of America, 112(15), E1898-E1907. https://doi.org/10.1073/pnas.1422238112
DOI https://doi.org/10.1073/pnas.1422238112
Keywords Glanzmann; Integrin; Single-nucleotide variants; Next-generation sequencing; Molecular modeling
Publisher URL https://www.pnas.org/content/112/15/E1898
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