Pathogenicity classification of variants associated with familial hypercholesterolemia: Comparison between guidelines

Background and Aims: Familial Hypercholesterolemia (FH) is a genetic dyslipidemia caused by pathogenic variants several genes (mainly LDLR, APOB and PCSK9). The presence of one or two pathogenic variants determine different disease form, the heterozygous (HeFH) and the homozygous one (HoFH). We aimed to perform a systematic reevaluation of all variants identified in 717 index patients. Methods: All identified variants (193) were classified according to the ACMG’s guidelines (Richards et al. 2015) and the most recent FH-specific suggestions (Chora et al. 2018 for APOB and PCSK9 and ClinGen – Chora et al. 2022 - for LDLR). Results: The most recent guidelines led to an increased number of LDLR variants classified as uncertain significance (VUS) respect to the general ones (38 vs 18 variants) and, conversely, a decreased number of pathogenic/likely pathogenic ones (92 vs 113 variants). The criteria most impacting the difference in classification are related with the functional characterization, the number of unrelated patients with the variant and the consideration of missense variants in LDLR. Four HoFH patients resulted reclassified as HeFH+USV, despite a clear variant/phenotype segregation among relatives. No differences were observed about 45 variants in APOB and 11 variants in PCSK9. Conclusions: New guidelines suggested FH-specific criteria useful for standardization of pathogenicity evaluation worldwide, although several variants resulted reclassified as USV. For rarest variants, guidelines could be improved giving more strength to the few available evidence, when no benignity criteria are present. The dissemination of frequency and segregation data present in molecular laboratory databases could improve the classification.