Expanding the genetics and phenotypic spectrum of Lysine-specific demethylase 5C (KDM5C): a report of 13 novel variants

• Published in: European journal of human genetics : EJHG 2023-02, Vol.31 (2), p.202-215
• Main Authors: Leonardi, Emanuela, Aspromonte, Maria Cristina, Drongitis, Denise, Bettella, Elisa, Verrillo, Lucia, Polli, Roberta, McEntagart, Meriel, Licchetta, Laura, Dilena, Robertino, D'Arrigo, Stefano, Ciaccio, Claudia, Esposito, Silvia, Leuzzi, Vincenzo, Torella, Annalaura, Baldo, Demetrio, Lonardo, Fortunato, Bonato, Giulia, Pellegrin, Serena, Stanzial, Franco, Posmyk, Renata, Kaczorowska, Ewa, Carecchio, Miryam, Gos, Monika, Rzońca-Niewczas, Sylwia, Miano, Maria Giuseppina, Murgia, Alessandra
• Format: Article
• Language: English
• Subjects: Asymptomatic; Chromatin; Chromatin remodeling; Dendritic plasticity; Female; Females; Frameshift Mutation; Gender differences; Genetics; Histone Demethylases - genetics; Histone Demethylases - metabolism; Hospitals; Humans; Hypertrichosis; Intellectual disabilities; Intellectual Disability - genetics; Lysine; Lysine - genetics; Male; Males; Mosaicism; Mutation; Neurodevelopmental disorders; Neuroplasticity; Neurosciences; Next-generation sequencing; Pediatrics; Proteins; Stop codon; X chromosomes; X-chromosome inactivation
• ISSN: 1018-4813; 1476-5438
• DOI: 10.1038/s41431-022-01233-4

Lysine-specific demethylase 5C (KDM5C) has been identified as an important chromatin remodeling gene, contributing to X-linked neurodevelopmental disorders (NDDs). The KDM5C gene, located in the Xp22 chromosomal region, encodes the H3K4me3-me2 eraser involved in neuronal plasticity and dendritic growth. Here we report 30 individuals carrying 13 novel and one previously identified KDM5C variants. Our cohort includes the first reported case of somatic mosaicism in a male carrying a KDM5C nucleotide substitution, and a dual molecular finding in a female carrying a homozygous truncating FUCA1 alteration together with a de novo KDM5C variant. With the use of next generation sequencing strategies, we detected 1 frameshift, 1 stop codon, 2 splice-site and 10 missense variants, which pathogenic role was carefully investigated by a thorough bioinformatic analysis. The pattern of X-chromosome inactivation was found to have an impact on KDM5C phenotypic expression in females of our cohort. The affected individuals of our case series manifested a neurodevelopmental condition characterized by psychomotor delay, intellectual disability with speech disorders, and behavioral features with particular disturbed sleep pattern; other observed clinical manifestations were short stature, obesity and hypertrichosis. Collectively, these findings expand the current knowledge about the pathogenic mechanisms leading to dysfunction of this important chromatin remodeling gene and contribute to a refinement of the KDM5C phenotypic spectrum.