Novel Variants Identified in Methyl-CpG-Binding Protein Genes in Autistic Individuals

Background: Misregulation of the methyl-CpG-binding protein 2 (MECP2) gene causes a myriad of neurodevelopmental disorders characterized by social and intellectual impairments - most notably Rett syndrome and some cases of autism.  We hypothesized that mutations in additional members of the methyl-CpG-binding family (MBD1, MBD2, MBD3 and MBD4) may also be involved in autistic spectrum disorders (ASD). This is further supported by evidence that different MBD proteins are capable of binding the same promoter region, suggesting a functional interdependence. To date, only one study has evaluated the MBD genes of autistic patients and was limited to a Japanese population. A single variation of interest was identified, R269C in MBD1.

Objectives: To evaluate the MBD1, MBD2, MBD3 and MBD4 genes for possible alterations that may be associated with autism.

Methods: In this study, 226 autistic individuals (195 Caucasians (CA) and 31 African-Americans (AA)) were evaluated for the coding regions of MBD1-4 by denaturing high performance liquid chromatography and results were confirmed either by TaqMan or direct sequencing. We used both multiplex and singleton families and examined transmission and disease concordance.  When available, additional family members were tested for segregation of variations identified in the proband.

Results: We identified 198 autistic individuals (167 CA and 31 AA) carrying genetic alterations at 46 unique loci. 20/46 of the variations were known single nucleotide polymorphisms (SNPs), while 26/46 were novel (5 insertion/deletions and 21 SNPs). While the majority of alterations were synonymous or noncoding SNPs, we identified 12 changes to amino acid sequence.  These encompassed 10 missense changes in MBD1, 3 and 4, a deletion of a single amino acid in MBD3, and a frameshift mutation in MBD4 that is predicted to truncate almost half of the protein.  Five of the nonsynonymous changes were found exclusively in singleton families.  The novel MBD3 R23M and E281del alterations were each found to segregate within the multiplex families where they were identified.  The MBD4 S342P variant was found to segregate in 4 of the 5 multiplex families in which it occurred and the remaining nonsynonymous changes did not consistently segregate.  We did not identify the MBD1 R296C variant.  Sixteen of the novel single nucleotide changes and four of the deletions were not found in 300 CA or 188 AA control alleles.  Furthermore, unaffected family members that also carry MBD variations present a range of psychiatric and developmental disorders including anxiety/panic disorder, depression, speech delay and learning disabilities.

Conclusions: We identified variations that could lead to alterations in RNA or protein structure and may result in functional changes.  Results from these rare variants indicate a potential role for the MBD genes in the molecular and genetic etiology of autism.