Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders

Hum Mol Genet. 2013 May 1;22(9):1816-25. doi: 10.1093/hmg/ddt035. Epub 2013 Jan 31.


The nonsense-mediated mRNA decay (NMD) pathway functions not only to degrade transcripts containing premature termination codons (PTC), but also to regulate the transcriptome. UPF3B and RBM8A, important components of NMD, have been implicated in various forms of intellectual disability (ID) and Thrombocytopenia with Absent Radius (TAR) syndrome, which is also associated with ID. To gauge the contribution of other NMD factors to ID, we performed a comprehensive search for copy number variants (CNVs) of 18 NMD genes among individuals with ID and/or congenital anomalies. We identified 11 cases with heterozygous deletions of the genomic region encompassing UPF2, which encodes for a direct interacting protein of UPF3B. Using RNA-Seq, we showed that the genome-wide consequence of reduced expression of UPF2 is similar to that seen in patients with UPF3B mutations. Out of the 1009 genes found deregulated in patients with UPF2 deletions by at least 2-fold, majority (95%) were deregulated similarly in patients with UPF3B mutations. This supports the major role of deletion of UPF2 in ID. Furthermore, we found that four other NMD genes, UPF3A, SMG6, EIF4A3 and RNPS1 are frequently deleted and/or duplicated in the patients. We postulate that dosage imbalances of these NMD genes are likely to be the causes or act as predisposing factors for neuro-developmental disorders. Our findings further emphasize the importance of NMD pathway(s) in learning and memory.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Case-Control Studies
  • Child
  • Codon, Nonsense
  • Computational Biology
  • DEAD-box RNA Helicases / genetics
  • DNA Copy Number Variations*
  • Developmental Disabilities / genetics*
  • Developmental Disabilities / pathology
  • Eukaryotic Initiation Factor-4A / genetics
  • Female
  • Gene Deletion
  • Gene Dosage
  • Genetic Predisposition to Disease
  • Humans
  • Intellectual Disability / genetics
  • Intellectual Disability / pathology
  • Male
  • Neurons / cytology*
  • Neurons / pathology
  • Nonsense Mediated mRNA Decay / genetics*
  • RNA, Messenger / genetics*
  • RNA-Binding Proteins / genetics
  • Ribonucleoproteins / genetics
  • Sequence Analysis, RNA
  • Telomerase / genetics
  • Transcription Factors / genetics
  • Transcriptome


  • Codon, Nonsense
  • RBM8A protein, human
  • RNA, Messenger
  • RNA-Binding Proteins
  • RNPS1 protein, human
  • Ribonucleoproteins
  • Transcription Factors
  • UPF2 protein, human
  • UPF3B protein, human
  • Eukaryotic Initiation Factor-4A
  • SMG6 protein, human
  • Telomerase
  • EIF4A3 protein, human
  • DEAD-box RNA Helicases