CTLA4 variant curation using adapted ACMG/AMP guidelines

Inborn errors of immunity (IEIs) are a group of heterogeneous diseases with broad phenotypes. Genetic testing has become the principal method of diagnosis for IEIs. However, confirmatory diagnostics rely on previous documentation of the variant, leaving clinicians and genetic counselors with a tremendous task when the variant is of uncertain significance (VUS) or with limited documentation. The American College of Medical Genetics and The Association for Molecular Pathology (ACMG/AMP) have published guidelines to determine whether a variant is pathogenic, VUS, or benign. However, in the context of IEIs, the ACMG/AMP guidelines might only fit partially due to the incomplete penetrance, high genetic heterogeneity, and extensive overlap between conditions seen in IEIs. For these reasons, the Antibody Deficiencies Variant Expert Panel (AD-VCEP, Table 1**) was created in 2021 to curate variants associated with IEIs. Each variant curated will reach FDA approval as part of the Clinical Genome Resource (ClinGen), an NIH-funded program to build a genomic knowledge base publicly available for laboratories, clinicians, and scientists.Table 1. Members of the Antibody Deficiency (AD) VCEPMemberRoleAmber Begtrup, PhD, FACMGCo-Chair, ExpertAnne Puel, PhD.Co-Chair, ExpertNeil Romberg, M.D.Co-Chair ExpertAlejandro Nieto, Ph.DCoordinatorAsbjorg Stray-Pederson, MD, PhD, FACMGExpertCindy Ma, PhDExpertMichael Jordan, MDExpertMenno van Zelm, PhDExpertBertrand Boisson, PhDExpertCarrie Lucas, PhDExpertJes Maimaris, PhDExpertIlenia SimeoniExpertCharlotte Cunningham-Rundles, MD, PhDExpertLijun Wang, MD, PhDExpertWilliam Hankey, PhDBiocuratorXiao Peng, MDBiocuratorLindsay Worley, BscBiocuratorAnnapoorni Lakshmansagar, MScBiocuratorKyle Hilliard, MScBiocuratorAlex Wonnaparhown, MDBiocuratorArtem Kalinichenko, PhDBiocurator Table 1. Members of the Antibody Deficiency (AD) VCEP The Antibody Deficiencies VCEP considers genes definitively associated with antibody immunodeficiencies, according to ClinGen. The first variants have been evaluated for autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency. The AD-VCEP has developed gene-specific variant curation rules for twenty different ACMG-AMP evidence codes considered applicable to the CTLA4 gene. Thirty CTLA4 variants have been selected for a pilot study of the rule specifications, with seventeen nominated as suspected pathogenic, five as suspected benign, and eight as variants of unknown significance. Rule specifications remain in the development stage of the ClinGen approval process. Still, preliminary results indicate that gene-specific modifications to the phenotype (PP4), population frequency (BS1, BA1), and hot spot (PM1) codes have significantly impacted the variant classifications outcome for CTLA4 insufficiency. Modifications have included creating a point system to define probands with a phenotype highly specific to the disorder, setting allele frequencies in control populations, and defining potential hot spots based on functional data. In summary, the work of this AD-VCEP represents the first comprehensive adaptation of the ACMG-AMP guidelines to the IEIs and will help to standardize IEI variant curation.