A rare GCH1 p.Arg170Gly variant shows impaired enzymatic activity and co-occurs with a novel NEXMIF p.Asp155GlnfsTer2 leading to a complex neurological phenotype: functional studies and clinical aspects

GTP cyclohydrolase I deficiency is a rare inherited disorder of biogenic amine metabolism due to pathogenic GCH1 variants, manifesting as DOPA-responsive dystonia or severe encephalopathy. Pathogenic variants in the NEXMIF gene cause X-linked intellectual disability and epilepsy. Here, using trio-WES approach, we identified a rare, previously uncharacterized GCH1 p.Arg170Gly variant and a novel NEXMIF p.Asp155GlnfsTer2 variant in a female patient. This study aimed to confirm the pathogenicity of these variants and elucidate their underlying molecular pathomechanisms by molecular in vitro studies. First, we confirmed that the NEXMIF variant introduces a premature stop codon at the cDNA level, implying loss of NEXMIF protein function. To explore the functional consequences of the GCH1 variant, we expressed and purified wild-type (WT) and p.Arg170Gly homodecameric GCH1, as well as a mixed population of heterodecameric GCH1 proteins, and performed biochemical characterization. Kinetic studies revealed that the catalytic efficiency of the mutant homo- and heterodecameric GCH1 was reduced by 37- and 9-fold, respectively, compared to the WT enzyme, confirming a significant loss of activity. Furthermore, the presence of mutant GCH1 monomers negatively affected catalytic cooperativity in the decameric enzyme. Circular dichroism indicated that p.Arg170Gly slightly impacts the structure of the protein, as shown by reduced α-helical content in the mutant homodecamer. In summary, we provide the first functional evidence that the GCH1 p.Arg170Gly variant is pathogenic mainly due to reduced enzyme activity, and that its combination with a novel NEXMIF loss-of-function variant manifests as a complex neurological phenotype arising from two distinct disorders.