De novo mutations in moderate or severe intellectual disability

PLoS Genet. 2014 Oct 30;10(10):e1004772. doi: 10.1371/journal.pgen.1004772. eCollection 2014 Oct.


Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Codon, Nonsense
  • Epilepsy / genetics*
  • Epilepsy / pathology
  • Exome / genetics
  • Frameshift Mutation
  • Humans
  • Intellectual Disability / genetics*
  • Intellectual Disability / pathology
  • Mutation, Missense
  • Point Mutation
  • RNA Splicing / genetics
  • Sequence Deletion


  • Codon, Nonsense