Frameshift variants in the UBTF gene are associated with neurodevelopmental disorders

The Upstream Binding Transcription Factor (UBTF) gene encodes a nucleolar phosphoprotein characterized by the presence of both DNA-binding and transactivation domains. Mutations in the UBTF gene have been implicated in a variety of pathological conditions. Specifically, recurrent de novo heterozygous missense mutations in UBTF have been linked to childhood onset neurodegeneration with brain atrophy, whereas UBTF haploinsufficiency has been associated with global developmental delay and distinctive facial features in the absence of neuroregression.

This study involved the recruitment of two unrelated individuals exhibiting psychomotor developmental delay and intellectual disability. Exome sequencing was performed to identify potential genetic variants. Additionally, RNA analysis was employed to assess the effects of these genetic variants on gene expression.

Both subjects demonstrated language impairments and intellectual disability without evidence of neuroregression. One individual experienced epilepsy and unilateral cerebellar dysplasia, while the other exhibited microcephaly, hypertonia, and psychosis. Genetic analysis identified two distinct frameshift variants in the UBTF gene, specifically c.2104del (p.Ser702Profs*83) and c.1199del (p.Gly400Alafs*38). RNA analysis of a peripheral blood sample demonstrated a decreased expression level of the mutant transcript. Furthermore, multiple alternative splicing events within the UBTF gene were observed in peripheral blood. Additionally, a systematic evaluation based on ClinGen criteria established a "Strong" gene-disease association between loss-of-function variants in UBTF and a neurodevelopmental delay without neuroregression.

The findings of this study expand the known genetic and phenotypic spectrum of neurological disorders associated with UBTF haploinsufficiency. These results contribute valuable insights toward elucidating the genotype-phenotype correlations underlying this condition.