Next-Generation Sequencing Reveals Novel Mutations in X-linked Intellectual Disability

Abstract

Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next-generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations. Studies have identified causal XLID genomic alterations in more than 100 protein-coding genes located on the X-chromosome. However, the causes for a substantial number of intellectual disability and associated phenotypes still remain unknown. Identification of causative genes and novel mutations will help in early diagnosis as well as genetic counseling of families. Advent of next-generation sequencing methods has accelerated the discovery of new genes involved in mental health disorders. In this study, we analyzed the exomes of three families from India with nonsyndromic XLID comprising seven affected individuals. The affected individuals had varying degrees of intellectual disability, microcephaly, and delayed motor and language milestones. We identified potential causal variants in three XLID genes, including PAK3 (V294M), CASK (complex structural variant), and MECP2 (P354T). Our findings reported in this study extend the spectrum of mutations and phenotypes associated with XLID, and calls for further studies of intellectual disability and mental health disorders with use of next-generation sequencing technologies.

Keywords: diagnostic medicine; genotype–phenotype association; mental retardation; neurodevelopmental disorders; next-generation sequencing.

FIG. 1.

XLID families. (A) Pedigrees of three XLID families from India. Solid red or green circles or boxes indicate sequenced samples. Genes with causal variants identified in each family are shown in the pedigree chart. (B) Flowchart depicting the joint variant calling and analysis performed on all the 15 samples studied. Causal variants identified following segregation analysis involving the family pedigree information is reported. NA, not available; XLID, X-linked intellectual disability.

FIG. 2.

PAK3 mutation. (A) Graphical representation of PAK3 protein showing the conserved protein domains. Mutations in PAK3 that have been previously reported to cause XLID are shown in black and the mutation identified in this study is shown in red. (B) PAK3 mutations shown in the context of structure of PAK3 kinase domain. Homology model was generated using the closely related PAK1 structure as a template. An ATP molecule model is shown in sticks. V294 is on the “roof” of the ATP binding site. (C) Multiple sequence alignment of PAK3 homologs showing the residues and conservation of the mutated valine 294 site (red) in PAK3.

FIG. 3.

Complex alteration in CASK. (A) Local alignment using Smith–Waterman algorithm of CASK sequences obtained from Sanger sequencing for the region that covers the complex alteration. (B) Known mutations depicted on a cartoon of CASK protein and its protein domains.