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

Abstract

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.

Keywords: DDX53; MSSNG; PTCHD1-AS; RNA helicase; SFARI; Xp22.11 locus; autism; autism spectrum disorder; neurodevelopmental disorders; non-coding RNA.

Graphical abstract

Figure 1

Summary of the genotypic and phenotypic features of the ASD-related Xp22.11 locus The Xp22.11 locus includes DDX53 (MIM: 301079), PTCHD1 (MIM: 300828), and the long noncoding RNA (lncRNA) PTCHD1-AS (PTCHD1 antisense RNA (head-to-head)). A number of deletions identified in male ASD participants (with whole-genome sequencing available from MSSNG, Simons Simplex Collection, and SPARK) were found to disrupt exons of the upstream lncRNA PTCHD1-AS and/or DDX53. PTCHD1-AS is categorized as “definitive” for ASD based on EAGLE gene curation and an SFARI gene score of 2, DDX53 has limited evidence for ASD based on EAGLE and an SFARI gene score of 2, and PTCHD1 has limited evidence for ASD based on EAGLE and an SFARI gene score of 1. ClinGen has determined PTCHD1 to be definitive for intellectual disability. SFARI Gene with curated EAGLE gene scores: https://gene.sfari.org/; ClinGen: https://clinicalgenome.org/.

Figure 2

Pedigrees of the reported families and genetic findings in all DDX53 participants (A) Pedigrees of the eight families showing the segregation of the DDX53 variants in affected individuals and the parents. All variants were inherited from unaffected mothers except the deletion identified in individual #9, which was inherited from the affected mother (#10) in family VIII. The carrier status is indicated by small filled circles. The mosaic status of the mother of the proband #5 is indicated by a small empty circle. (B) Schematic representation of the total of the DDX53 variants mapped to the unique protein isoform (NP_874358.2). The variants identified in the described families and those identified in participants from the SFARI and MSSNG databases are reported in blue and black, respectively. DEXDc, DEAD-like helicase superfamily domain; HELICc, helicase conserved C-terminal domain; KH, K homology domain.

Figure 3

Graphic representation of intolerance to DDX53 variants Using the Metadome software (https://stuart.radboudumc.nl/metadome/), we mapped the variants identified in our cohort and in the SFARI and MSSNG datasets to DDX53. The purple segments indicate the main functional domains of the protein: KH, DEXDc, and HELICc, respectively. Affected amino acids are highlighted in green. Most variants were found to affect amino acid residues that showed intolerance to variation according to their variation in the gnomAD dataset. The residues affected by DDX53 variants are very rarely or not impacted at all by genetic changes observed in gnomAD 4.1.0.

Figure 4

Graphical representation of human, mouse, and rat syntenic regions and breaks in chrX:10,445,310–35,803,753 (GRCh38) (A) Syntenic alignment between human and mouse show inverted orientation of two corresponding segments between human and mouse. Syntenic alignment between human and rat is shown to highlight the mouse-specific inversion of this chromosomal segment and the shared syntenic break located just upstream of PTCHD1. (B) Inset of human-mouse syntenic region at the PTCHD1-AS locus. (C) Phylogenetic tree of DDX53 and DDX43 created by Treefam. Red triangle denotes a duplication event. Green circle denotes a speciation event. The colored segments represent the main functional domains of the protein: KH (green), DEXDc (pink), and HELICc (blue), respectively. (D) Phylogenetic tree of DDX53 and DDX43 in common model organisms.