Donor splice-site mutation in CUL4B is likely cause of X-linked intellectual disability

Abstract

X-linked intellectual disability is the most common form of cognitive disability in males. Syndromic intellectual disability encompasses cognitive deficits with other medical and behavioral manifestations. Recently, a large family with a novel form of syndromic X-linked intellectual disability was characterized. Eight of 24 members of the family are male and had cognitive dysfunction, short stature, aphasia, skeletal abnormalities, and minor anomalies. To identify the causative gene(s), we performed exome sequencing in three affected boys, both parents, and an unaffected sister. We identified a haplotype consisting of eight variants located in cis within the linkage region that segregated with affected members in the family. Of these variants, two were novel. The first was at the splice-donor site of intron 7 (c.974+1G>T) in the cullin-RING ubiquitin ligase (E3) gene, CUL4B. This variant is predicted to result in failure to splice and remove intron 7 from the primary transcript. The second variant mapped to the 3'-UTR region of the KAISO gene (c.1127T>G). Sanger sequencing validated the variants in these relatives as well as in three affected males and five carriers. The KAISO gene variant was predicted to create a binding site for the microRNAs miR-4999 and miR-4774; however, luciferase expression assays failed to validate increased targeting of these miRNAs to the variant 3'-UTR. This SNP may affect 3'-UTR structure leading to decreased mRNA stability. Our results suggest that the intellectual disability phenotype in this family is caused by aberrant splicing and removal of intron 7 from CUL4B gene primary transcript.

Keywords: X-linked; exome sequencing; intellectual disability.

FIG. 1

Pedigree of the extended family with the XLID phenotype (A). The six members of the family for whom exome sequencing was performed are highlighted in the red box. Sanger sequencing was performed to validate the identified variants in the CUL4B gene (B) and the KAISO gene (C). Sanger sequencing of the two variants was performed also on members of the extended family, and those containing the two variants are highlighted (asterisk).

FIG. 2

Shown is a schematic representation of the genomic structure of the CUL4B gene with all the locations of the previously characterized mutations. The splice-site mutation identified here is highlighted.