PRF1 – Familial Hemophagocytic Lymphohistiocytosis Type 2

Perforin, encoded by PRF1, is a pore-forming protein essential for lymphocyte-mediated cytotoxicity. Biallelic pathogenic variants in PRF1 cause Familial Hemophagocytic Lymphohistiocytosis Type 2 (MONDO:0011337), an autosomal recessive immunodeficiency presenting with fever, hepatosplenomegaly, cytopenias and hemophagocytosis.

A comprehensive review of over 100 unrelated probands across more than 50 families has identified a broad spectrum of PRF1 variants, including frameshift deletions (e.g., c.65delC), nonsense mutations (e.g., c.1A>G), and missense substitutions (e.g., c.272C>T (p.Ala91Val)) (PMID:12060139; PMID:15755897). Segregation studies in multiple consanguineous and non-consanguineous pedigrees confirm autosomal recessive inheritance, with at least six affected relatives showing co-segregation of biallelic variants and clinical disease.

Functional analyses demonstrate that PRF1 mutations lead to absent or markedly reduced intracellular perforin expression in NK and CD8+ T cells, severely impaired cytotoxicity in vitro, and, in some missense cases, partial recovery of function upon IL-2 stimulation (PMID:23073290). Structural and biophysical studies classify missense alleles by their effects on perforin maturation and stability, supporting a dose-dependent mechanism of haploinsufficiency.

The recurrent variant c.272C>T (p.Ala91Val) exemplifies this mechanism: first considered a benign polymorphism, it exhibits reduced perforin levels and cytotoxic function in compound heterozygotes, correlating with late-onset or attenuated FHL2 phenotypes (PMID:23073290). Population data show variable penetrance, underscoring the need for combined genetic and functional assays in carrier assessment and prenatal counseling.

Integration of genetic and experimental evidence fulfils the ClinGen criteria for a Definitive gene–disease association. Genetic evidence is Strong: >100 probands with biallelic variants, robust segregation, and multiple variant classes reaching the genetic cap. Functional evidence is Strong: concordant cellular assays, flow cytometry, and rescue experiments consistently demonstrate impaired perforin function.

Key Take-home: Early PRF1 sequencing and perforin flow‐cytometry are critical for prompt diagnosis of FHL2 and guide timely hematopoietic stem cell transplantation to improve survival.

References

• British journal of haematology | 2002 | Functional consequences of perforin gene mutations in 22 patients with familial haemophagocytic lymphohistiocytosis PMID:12060139
• Blood | 2005 | A functional analysis of the putative polymorphisms A91V and N252S and 22 missense perforin mutations associated with familial hemophagocytic lymphohistiocytosis PMID:15755897
• Human immunology | 2013 | Functional impact of A91V mutation of the PRF1 perforin gene PMID:23073290

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