Specifications of the variant curation guidelines for ITGA2B/ITGB3: ClinGen Platelet Disorder Variant Curation Panel

Abstract

Accurate and consistent sequence variant interpretation is critical to the correct diagnosis and appropriate clinical management and counseling of patients with inherited genetic disorders. To minimize discrepancies in variant curation and classification among different clinical laboratories, the American College of Medical Genetics and Genomics (ACMG), along with the Association for Molecular Pathology (AMP), published standards and guidelines for the interpretation of sequence variants in 2015. Because the rules are not universally applicable to different genes or disorders, the Clinical Genome Resource (ClinGen) Platelet Disorder Expert Panel (PD-EP) has been tasked to make ACMG/AMP rule specifications for inherited platelet disorders. ITGA2B and ITGB3, the genes underlying autosomal recessive Glanzmann thrombasthenia (GT), were selected as the pilot genes for specification. Eight types of evidence covering clinical phenotype, functional data, and computational/population data were evaluated in the context of GT by the ClinGen PD-EP. The preliminary specifications were validated with 70 pilot ITGA2B/ITGB3 variants and further refined. In the final adapted criteria, gene- or disease-based specifications were made to 16 rules, including 7 with adjustable strength; no modification was made to 5 rules; and 7 rules were deemed not applicable to GT. Employing the GT-specific ACMG/AMP criteria to the pilot variants resulted in a reduction of variants classified with unknown significance from 29% to 20%. The overall concordance with the initial expert assertions was 71%. These adapted criteria will serve as guidelines for GT-related variant interpretation to increase specificity and consistency across laboratories and allow for better clinical integration of genetic knowledge into patient care.

Graphical abstract

Figure 1.

Schematic representation of integrin αIIbβ3 major domains in relation to 70 pilot variants with their final PD-EP classification. Integrin αIIbβ3 subunits αIIb (top) and β3 (bottom) each possess a signal peptide (SP), an extracellular domain involved in ligand binding (β propeller and βI, respectively), a transmembrane (TM) domain, and a cytoplasmic domain (C). Clinically actionable variants (PATH, LPATH) are shown above the protein schematics; VUS, LBEN, and BEN variants are shown below.

Figure 2.

PVS1 decision tree for ITGA2B/ITGB3 variants. Application of different levels of strength for PVS1 depending on the following factors: type of variant (light blue), prediction of nonsense-mediated decay (NMD; gray), location within a known critical protein domain (green), and size of deletion (yellow). N/A, not applicable.

Figure 3.

PP4 decision tree for GT patients. Application of different levels of strength for PP4 depending on bleeding and laboratory phenotypes, analysis of αIIbβ3 expression or function, and sequencing coverage.

Figure 4.

Summary of the variant interpretation criteria applied to the 70 ITAG2B/ITGB3 validation variants. The frequency with which PD-EP–specified ACMG/AMP criteria were applied during the variant pilot. Several criteria were applied at varying levels of strength, as indicated by shading (legend on the right). A majority of rules were applied at least once; however, no relevant variants were identified for application of PS1, PM6, BS2, BS4, or BP3 criteria.

Figure 5.

Comparison of initial expert assertions and final PD-EP classifications of the 70 ITAG2B/ITGB3 validation variants. The total height of each bar represents the number of variants with each initial assertion. The colored segments of each bar represent the final PD-EP classification (legend on the right).