In Silico Investigation of a Missense Mutation in CLIC2 Associated with Intellectual Disability

Abstract

While numerous nsSNPs (nonsynonomous SNP) have been reported in the CLIC2 gene in healthy individuals (indicating that the CLIC2 protein can tolerate amino acid substitutions while still being fully functional), we recently identified a missense mutation in CLIC2 on Xq28 in a male with X-linked intellectual disability (XLID). This mutation, c.303C>G (p.H101Q), was not observed in 1059 control X chromosomes, which indicates that it may contribute to intellectual disability. To test the possibility that p.H101Q is a disease-causing mutation, we performed extensive in silico simulations to calculate the effects caused by the p.H101Q mutation on CLIC2 stability, dynamics, and ionization states. We then compared the effects obtained for the (presumably) harmless nsSNPs. In silico analysis predicted that p.H101Q, in contrast with other nsSNPs, (a) reduces the flexibility of the joint loop which is important for the normal function of CLIC2, (b) makes the overall 3D structure of CLIC2 more stable and thus reduces the possibility of the large conformational change expected to occur from the soluble to membrane state of CLIC2, and (c) removes the positively charged residue, H101, from the joint loop which may be important for the membrane association of CLIC2. The results of the in silico modeling, in conjunction with the polymorphism analysis, suggest that p.H101Q is indeed a disease-causing mutation, which is the first one found in the family of the CLIC proteins. This work was supported by awards from NLM/NIH, grant numbers 1R03LM009748 and 1R03LM009748-S1.