CXorf56, a dendritic neuronal protein, identified as a new candidate gene for X-linked intellectual disability

Abstract

Intellectual disability (ID) comprises a large group of heterogeneous disorders, often without a known molecular cause. X-linked ID accounts for 5-10% of male ID cases. We investigated a large, three-generation family with mild ID and behavior problems in five males and one female, with a segregation suggestive for X-linked inheritance. Linkage analysis mapped a disease locus to a 7.6 Mb candidate region on the X-chromosome (LOD score 3.3). Whole-genome sequencing identified a 2 bp insertion in exon 2 of the chromosome X open reading frame 56 gene (CXorf56), resulting in a premature stop codon. This insertion was present in all intellectually impaired individuals and carrier females. Additionally, X-inactivation status showed skewed methylation patterns favoring the inactivation of the mutated allele in the unaffected carrier females. We demonstrate that the insertion leads to nonsense-mediated decay and that CXorf56 mRNA expression is reduced in the impaired males and female. In murine brain slices and primary hippocampal neuronal cultures, CXorf56 protein was present and localized in the nucleus, cell soma, dendrites, and dendritic spines. Although no other families have been identified with pathogenic variants in CXorf56, these results suggest that CXorf56 is the causative gene in this family, and thus a novel candidate gene for X-linked ID with behavior problems.

Non‐syndromic X linked intellectual disability: Current knowledge in light of the recent advances in molecular and functional studies

“…The last XLID update published, estimated that 141 genes are associated with XLID. Since then, more genes have been associated to XLID such as CXorf56 , HS6ST2 , NAA15 , POLA1 and SLC9A7 (Figure ). However, the link of some of these genes to XLID is still questionable .…”

Novel clinical and genetic insight into CXorf56-associated intellectual disability

“…In our patients, an in-frame deletion of two residues and an insertion-deletion leading to a frameshift and premature stop were identified. Both variants are located more C-terminal (exons 4 and 5) to the previously reported variant by Verkerk et al (exon 2) [5], which was shown to be subjected to NMD, with loss-of-function as the likely disease mechanism. The newly described variants are inferred to lead to LoF.…”

“…The previously reported female by Verkerk et al presented mainly with moderate ID, behavioral issues, and mild dysmorphic features. X-chromosome inactivation analysis did not show a skewed methylation pattern (54%) in the affected female, while six unaffected female carriers showed a 76-93% inactivation of the maternally inherited allele [5]. X-methylation analyses in three females from family 1 (two mildly affected and one unaffected) confirmed skewed X-inactivation in blood cells from mildly symptomatic females (97 and 83%, II-2 and II-6), while 100% skewed X-inactivation pattern of the putative carrier chromosome was observed in the asymptomatic female (I-2).…”

“…Recently, Verkerk et al [5], described CXorf56 as a new candidate gene for ID in a large family with mild X-linked ID (four males and one female). These five patients presented with nonsyndromic ID and behavioral issues.…”

“…Via linkage analysis followed by whole genome sequencing, the authors uncovered a frameshift variant in exon 2 of CXorf56 (NM_022101.3c.159_160insTA) that leads to nonsensemediated decay (NMD) with reduced mRNA expression in the affected individuals. No other patients with CXorf56 causative variants were identified among 413 unrelated individuals with ID without specific diagnosis [5].…”