Genetic variants in DDX53 contribute to autism spectrum disorder associated with the Xp22.11 locus

• Published in: American journal of human genetics Vol. 112; no. 1; pp. 154 - 167
• Main Authors: Scala, Marcello, Bradley, Clarrisa A., Howe, Jennifer L., Trost, Brett, Salazar, Nelson Bautista, Shum, Carole, Mendes, Marla, Reuter, Miriam S., Anagnostou, Evdokia, MacDonald, Jeffrey R., Ko, Sangyoon Y., Frankland, Paul W., Charlebois, Jessica, Elsabbagh, Mayada, Granger, Leslie, Anadiotis, George, Pullano, Verdiana, Brusco, Alfredo, Keller, Roberto, Parisotto, Sarah, Pedro, Helio F., Lusk, Laina, McDonnell, Pamela Pojomovsky, Helbig, Ingo, Mullegama, Sureni V., Douine, Emilie D., Corona, Rosario Ivetth, Russell, Bianca E., Nelson, Stanley F., Graziano, Claudio, Schwab, Maria, Simone, Laurie, Zara, Federico, Scherer, Stephen W.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 02.01.2025; Elsevier
• Subjects: Adolescent; Adult; autism; autism spectrum disorder; Autism Spectrum Disorder - genetics; Child; Child, Preschool; Chromosomes, Human, X - genetics; DDX53; DEAD-box RNA Helicases - genetics; Female; Genetic Loci; Genetic Predisposition to Disease; Genetic Variation; Humans; Male; MSSNG; neurodevelopmental disorders; non-coding RNA; Pedigree; PTCHD1-AS; RNA helicase; RNA, Long Noncoding - genetics; SFARI; Xp22.11 locus; PTCHD1-AS; MSSNG; non-coding RNA; SFARI; DDX53; Xp22.11 locus; autism spectrum disorder; neurodevelopmental disorders; autism; RNA helicase
• ISSN: 0002-9297; 1537-6605; 1537-6605
• DOI: 10.1016/j.ajhg.2024.11.003

Autism spectrum disorder (ASD) exhibits an ∼4:1 male-to-female sex bias and is characterized by early-onset impairment of social/communication skills, restricted interests, and stereotyped behaviors. Disruption of the Xp22.11 locus has been associated with ASD in males. This locus includes the three-exon PTCHD1, an adjacent multi-isoform long noncoding RNA (lncRNA) named PTCHD1-AS (spanning ∼1 Mb), and a poorly characterized single-exon RNA helicase named DDX53 that is intronic to PTCHD1-AS. While the relationship between PTCHD1/PTCHD1-AS and ASD is being studied, the role of DDX53 has not been comprehensively examined, in part because there is no apparent functional murine ortholog. Through clinical testing, here, we identified 8 males and 2 females with ASD from 8 unrelated families carrying rare, predicted damaging or loss-of-function variants in DDX53. Additionally, we identified a family consisting of a male proband and his affected mother with high-functioning autism, both harboring a gene deletion involving DDX53 and exons of the noncoding RNA PTCHD1-AS. Then, we examined databases, including the Autism Speaks MSSNG and Simons Foundation Autism Research Initiative, as well as population controls. We identified 26 additional individuals with ASD harboring 19 mostly maternally inherited, rare, damaging DDX53 variations, including two variants detected in families from the original clinical analysis. Our findings in humans support a direct link between DDX53 and ASD, which will be important in clinical genetic testing. These same autism-related findings, coupled with the observation that a functional orthologous gene is not found in mice, may also influence the design and interpretation of murine modeling of ASD. [Display omitted] In this study, we identify rare variants in DDX53 as relevant contributors to autism spectrum disorder (ASD) associated with the Xp22.11 locus. Our findings support a direct link between DDX53 and ASD with important implications for clinical genetic testing and the design/interpretation of murine modeling of ASD.