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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.

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