Glanzmann Thrombasthenia Caused by an 11.2-kb Deletion in the Glycoprotein IIIa (β3 ) Is a Second Mutation in Iraqi Jews That Stemmed From a Distinct Founder

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

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.

The Human Platelet IIb Gene Is Not Closely Linked to Its Integrin Partner β3

IIbb3 integrin is a heterodimeric receptor facilitating platelet aggregation. Both genes are on chromosome 17q21.32. Intergenic distance between them has been reported to be 125 to 260 kilobasepairs (kb) by pulsed-field gel electrophoresis (PFGE) genomic analysis, suggesting that they may be regulated coordinately during megakaryopoiesis. In contrast, other studies suggest these genes are greater than 2.0 megabasepairs (mb) apart. Because of the potential biological implications of having these two megakaryocytic-specific genes contiguous, we attempted to resolve this discrepancy. Taking advantage of large kindreds with mutations in either IIb or β3, we have developed a genetic linkage map between the thyroid receptor hormone-1 gene (THRA1) and β3 as follows: cen-THRA1-BRCA1-D17S579/IIb-β3-qter, with a distance of 1.3 centiMorgans (cM) between IIb and β3 and the two genes being oriented in the same direction. PFGE genomic and YAC clone analysis showed that the β3 gene is distal and ≥365 kb upstream of IIb. Additional restriction mapping shows IIb is linked to the erythrocyte band 3 (EPB3) gene, and β3 to the homeobox HOX2b gene. Analysis of IIb+-BAC and P1 clones confirm that the EPB3 gene is ∼110 kb downstream of the IIb gene. Sequencing the region surrounding the human IIb locus showed the Granulin gene ∼18 kb downstream to IIb, and the KIAA0553 gene ∼5.7 kb upstream. This organization is conserved in the murine sequence. These studies show that IIb and β3 are not closely linked, with IIb flanked by nonmegakaryocytic genes, and imply that they are unlikely to share common regulatory domains during megakaryopoiesis.