A CHD7 intronic variant induces aberrant splicing and structural alterations in the CHD7 DNA-binding domain to cause CHARGE syndrome.

Abstract

Objectives: CHARGE syndrome (CS), a rare inherited condition, is mainly caused by pathogenic variants in the gene encoding chromodomain helicase DNA-binding protein 7 (CHD7). In the present investigation, the genetic etiology of CS was elucidated in a Chinese patient presenting with characteristic clinical features.

Methods: A 28-year-old female with amenorrhea, facial asymmetry, right ear malformation, hearing impairment, and congenital cardiac anomalies was evaluated using whole-exome sequencing (WES) for mutation screening. Familial Sanger sequencing subsequently confirmed the identified variant as de novo. Minigene assays were used to assess the pathogenicity of the splicing variant, while the structural alterations in CHD7 were characterized using computational modeling and electrostatic potential analyses.

Results: WES detected a heterozygous CHD7 splice-site variant, c.5405-17 G>A, which was not detected in either parent. Minigene-based functional assessments revealed this de novo CHD7 variant to cause a 15-bp insertion, resulting in a five-amino-acid insertion between the helicase and the SANT domains of CHD7, thereby potentially altering DNA binding. Hormone replacement therapy successfully induced cyclic menstruation, and surgical intervention corrected the auricular deformity.

Conclusions: A de novo pathogenic splice-site mutation (c.5405-17 G>A) was identified in this study, which leads to the pathogenesis of CS. Subsequent functional evaluation confirmed that this mutation disrupts normal mRNA processing, thereby inducing structural alterations in the CHD7 protein. The results obtained herein advance our understanding of the mutational spectrum of CHD7, while emphasizing the importance of combining clinical, genetic, and functional analyses for the definitive diagnosis of CS.