High proportion of 22q13 deletions and SHANK3 mutations in Chinese patients with intellectual disability

Abstract

Intellectual disability (ID) is a heterogeneous disorder caused by chromosomal abnormalities, monogenic factors and environmental factors. 22q13 deletion syndrome is a genetic disorder characterized by severe ID. Although the frequency of 22q13 deletions in ID is unclear, it is believed to be largely underestimated. To address this issue, we used Affymetrix Human SNP 6.0 array to detect the 22q13 deletions in 234 Chinese unexplained ID patients and 103 controls. After the Quality Control (QC) test of raw data, 22q13 deletions were found in four out of 230 cases (1.7%), while absent in parents of the cases and 101 controls. A review of genome-wide microarray studies in ID was performed and the frequency of 22q13 deletions from the literatures was 0.24%, much lower than our report. The overlapping region shared by all 4 cases encompasses the gene SHANK3. A heterozygous de novo nonsense mutation Y1015X of SHANK3 was identified in one ID patient. Cortical neurons were prepared from embryonic mice and were transfected with a control plasmid, shank3 wild-type (WT) or mutant plasmids. Overexpression of the Y1015 mutant in neurons significantly affected neurite outgrowth compared with shank3 WT. These findings suggest that 22q13 deletions may be a more frequent cause for Chinese ID patients than previously thought, and the SHANK3 gene is involved in the neurite development.

Figure 1. High-density SNP-array Analysis of Chromosome 22q13 Deletions in Four Patients with ID.

Microdeletions and duplications are represented by red and blue bars respectively. Annotated genes in the overlapping region are shown in the bottom of the figure.

Figure 2. Identification and functional analysis of SHANK3 mutations.

(A) Pedigree of the proband with a de novo Y1015X mutation and localization of this nonsense variation on the linear protein structure of SHANK3. ANK, ankyrin repeats; SH3, Src homology 3 domain; PDZ, postsynaptic density protein; SAM, sterile α motif domain. (B) Representative photographs demonstrating the anatomic differences in traced neurons transfected with empty vector, SHANK3 WT, A921T, or Y1015X vectors, respectively. (C–F) Analysis of SHANK3 mutations in primary mouse cortical neuronal cultures. Neurite number (C), nodes (D), tips (E) and total length (F) are quantified in bar histograms along with standard error of the mean for each bar. Asterisks indicate a statistically significant difference (**P<0.001, Post Hoc tests). Compared to control, WT and A921T, the overexpression of Y1015X significantly decreased neurite complexity and length.