Severe nonketotic hyperglycinaemia due to a synonymous variant

Nonketotic hyperglycinaemia (NKH) is an autosomal recessive neurometabolic disorder resulting from deficient glycine cleavage system activity, causing severe neurological impairment. While NKH is typically associated with pathogenic variants in glycine decarboxylase (GLDC) or aminomethyltransferase, the role of synonymous variants remains uncertain. To date, no cases of NKH caused by GLDC homozygous synonymous variants have been reported. Herein, a female infant born to consanguineous parents who developed refractory seizures, progressing to infantile epileptic spasms syndrome at 2 months is reported. Initial genetic testing identified a homozygous synonymous GLDC variant (c.1023G > A, p.Val341=), previously classified as “likely benign” in ClinVar (variation identification number: 1108119). Minigene splicing analysis revealed that the c.1023G > A variant caused a 38-base pair deletion in exon 7 (r.1021_1058del), Given the phenotypic characteristics of the child, we predict that this may resulting in a frameshift mutation (p.Val341ArgfsTer56) and a truncated protein. This functional evidence confirmed the pathogenicity of the variant.