Contribution of SHANK3 mutations to autism spectrum disorder

Abstract

Mutations in SHANK3, which encodes a synaptic scaffolding protein, have been described in subjects with an autism spectrum disorder (ASD). To assess the quantitative contribution of SHANK3 to the pathogenesis of autism, we determined the frequency of DNA sequence and copy-number variants in this gene in 400 ASD-affected subjects ascertained in Canada. One de novo mutation and two gene deletions were discovered, indicating a contribution of 0.75% in this cohort. One additional SHANK3 deletion was characterized in two ASD-affected siblings from another collection, which brings the total number of published mutations in unrelated ASD-affected families to seven. The combined data provide support that haploinsufficiency of SHANK3 can cause a monogenic form of autism in sufficient frequency to warrant consideration in clinical diagnostic testing.

Figure 1.

Pedigrees of the ASD-affected families with de novo variants or unbalanced translocation derivatives. Arrows denote the index subject. In ASD1, the proband has a de novo 277-kb deletion at 22q13.33 and a de novo 1.4-Mb duplication at 20q13.33. In ASD2, the father carries a balanced translocation t(14;22)(q32.33;q13.31); the elder daughter with ASD has inherited the der(22) t(14;22)(q32.33;q13.31), whereas the younger daughter with ADHD inherited the der(14) t(14;22)(q32.33;q13.31). In ASD3, both children have a de novo 4.4-Mb deletion at 22q13.31-33. In ASD4, the proband has a de novo Q321R mutation. The diamond indicates three siblings without ASD who were unavailable for sampling.

Figure 2.

A, Copy-number analysis of ASD3 showing 4.4-Mb deletion at 22q13.31-q13.33. The genomic coordinates are shown at the top, with red dots and blue lines showing raw and smoothed intensities, respectively. The blue bar at the bottom is indicative of homozygous SNP calls. B, Quantitative PCR results depicting 277-kb loss in ASD1, where both parents and siblings are copy neutral. C, FISH analysis of the de novo deletion of the SHANK3 region in ASD1. The red signal (SHANK3 probe G248P86064C8) is deleted, and the green signal is a control probe mapping to chromosome 14 (RP11-652N16). D, Sequencing showing de novo A962G change in the ASD4 proband.

Figure 3.

Mutations and variations of SHANK3. The top half gives the location of the mutations and rare nonsynonymous variations found in the present study, whereas the bottom half shows those described elsewhere. De novo mutations are shown in bold. SH3 = Src homology-3 domain; PDZ = PDZ domain; H = homer–binding site; C = cortactin-binding site; SAM = sterile α motif.