NM_000277.3(PAH):c.1316-1G>A

For PAH c.1316-1G>A, a canonical splice acceptor variant predicted to abolish normal exon 12 inclusion and produce non-functional PAH enzyme, liver-directed AAV gene therapy delivering a functional PAH transgene is a rational therapeutic approach. This variant disrupts the invariant AG dinucleotide at the exon 12 splice acceptor site, expected to cause exon skipping or intron retention and consequent loss of phenylalanine hydroxylase activity. Because splice-site variants are not amenable to simple base editing (unlike point missense variants), gene addition via AAV is the most straightforward precision medicine approach for this allele. Multiple AAV-PAH programs are in preclinical to early clinical development, with mouse models demonstrating sustained normalization of blood phenylalanine following liver-directed AAV5 or AAV8 gene transfer.

AAV-mediated liver-directed PAH gene addition has shown preclinical proof-of-concept in Pah-enu2 mice, with sustained phenylalanine normalization lasting months after a single administration (Viecelli et al., Nat Med 2014; PMID:25100528). BioMarin BMN 307 (AAV5-PAH) entered Phase 1/2 clinical trials (NCT04480567), representing the most advanced AAV gene therapy for PKU, though the program was subsequently paused. Additional approaches using mRNA-LNP for transient PAH expression are in development (Brooks et al., HGG Adv 2024; PMID:37922902). For c.1316-1G>A specifically, this splice-site variant is classified as Pathogenic in ClinVar. The invariant G at position -1 of the splice acceptor is critical for spliceosome recognition; G>A substitution at this position has well-established precedent across multiple genes for causing complete exon skipping. In compound heterozygotes, the second allele genotype modulates phenotype severity, but patients homozygous or compound heterozygous for null alleles like splice-site variants typically present with classical PKU requiring strict dietary phenylalanine restriction.

BMN 307, the most advanced AAV-PAH program, was paused due to hepatocellular carcinoma signals in a mouse study, raising concerns about insertional mutagenesis risk with AAV integration in dividing hepatocytes. Whether these mouse findings translate to human risk remains debated, as the Pah-enu2 mouse model has inherent liver pathology. Pre-existing anti-AAV antibodies exclude a significant fraction of patients from AAV gene therapy. Transgene expression durability is uncertain — episomal AAV genomes may be diluted with hepatocyte turnover, particularly in pediatric patients with growing livers, potentially requiring retreatment that is precluded by anti-AAV immunity. For a splice-site variant like c.1316-1G>A, direct correction approaches (e.g., U1 snRNA modification or splice-switching ASOs) could theoretically restore normal splicing but remain preclinical. The dietary management alternative, while burdensome, is effective at preventing intellectual disability if initiated early, making the risk-benefit calculus for gene therapy more complex than for diseases without existing treatment options.