Beyond genotype: challenges in predicting disease risk for carriers of biallelic perforin variants

• Variable penetrance of A91V/pLOF PRF1 genotypes complicates disease prediction.

• Functional assays do not reliably predict clinical outcome.

Genetic screening for severe congenital immuno-hematological diseases offers potential for early intervention, particularly through preemptive allogeneic stem cell transplantation (HSCT). However, the clinical value of such screening depends on precise prognostic predictions based on genotype-phenotype correlations and/or functional confirmation. We investigated familial hemophagocytic lymphohistiocytosis type 2 (FHL2), caused by PRF1 variants. Specifically we evaluated the clinical significance of the frequent PRF1 A91V variant, if present in trans with a predicted loss-of-function (pLOF) PRF1 variant, defined as "disease mutation" listed in the Human Gene Mutation Database. We combined clinical and functional data from our HLH-network registry with UK Biobank data to evaluate disease penetrance and clinical outcomes. Among 52 A91V/pLOF individuals in the registry, 39 (72%) showed FHL2-related manifestations with mean onset at 20 years. Four patients had recurrent disease, 15 were transplanted, and 14 died. Among 14 A91V/pLOF individuals identified by family screening (mean 29 years), however, only one was symptomatic. Moreover, among 21 A91V/pLOF carriers identified in 200,000 UK Biobank participants, 12 with genotypes identical to symptomatic registry patients, none had developed HLH by age 73. Premature stop pLOF alleles appeared more penetrant than missense variants, but functional data including perforin expression or cytotoxicity failed to predict disease manifestation. Our combined registry and population-based approach reveals significant variability in disease penetrance and severity among PRF1 A91V/pLOF carriers, with no clear association between genotype, functional data and clinical outcomes. This complexity illustrates the challenges of genetic screening and highlights the need for careful clinical decision-making regarding preemptive HSCT in asymptomatic carriers.