Novel Missense Mutation A789V in IQSEC2 Underlies X-Linked Intellectual Disability in the MRX78 Family.

Vera M Kalscheuer,Robert J Harvey,Miranda L Himelright,Hao Hu,Philip Long,Melanie Bienek,Victoria M James,Renske Oegema,A Jeannette M Hoogeboom,Maya Topf,Corinna Jensen,Randall Walikonis,Stefan A Haas,Kirsten Harvey

doi:10.3389/fnmol.2015.00085

Abstract

Disease gene discovery in neurodevelopmental disorders, including X-linked intellectual disability (XLID) has recently been accelerated by next-generation DNA sequencing approaches. To date, more than 100 human X chromosome genes involved in neuronal signaling pathways and networks implicated in cognitive function have been identified. Despite these advances, the mutations underlying disease in a large number of XLID families remained unresolved. We report the resolution of MRX78, a large family with six affected males and seven affected females, showing X-linked inheritance. Although a previous linkage study had mapped the locus to the short arm of chromosome X (Xp11.4-p11.23), this region contained too many candidate genes to be analyzed using conventional approaches. However, our X-chromosome exome resequencing, bioinformatics analysis and inheritance testing revealed a missense mutation (c.C2366T, p.A789V) in IQSEC2, encoding a neuronal GDP-GTP exchange factor for Arf family GTPases (ArfGEF) previously implicated in XLID. Molecular modeling of IQSEC2 revealed that the A789V substitution results in the insertion of a larger side-chain into a hydrophobic pocket in the catalytic Sec7 domain of IQSEC2. The A789V change is predicted to result in numerous clashes with adjacent amino acids and disruption of local folding of the Sec7 domain. Consistent with this finding, functional assays revealed that recombinant IQSEC2A789V was not able to catalyze GDP-GTP exchange on Arf6 as efficiently as wild-type IQSEC2. Taken together, these results strongly suggest that the A789V mutation in IQSEC2 is the underlying cause of XLID in the MRX78 family.

Highlights

Intellectual disability (ID) is a developmental brain disorder characterized by impaired intellectual and adaptive functions, and can be defined by an IQ below 70 and limitations in intellectual functioning and adaptive behaviors
This study reports the identification and functional characterization of a novel mutation (c.C2366T, p.A789V) in IQSEC2 that based on variant filtering and segregation analysis likely presents the cause of X-linked intellectual disability (XLID) in the large family MRX78
Using molecular modeling of wild-type and mutant protein and assays for ArfGEF activity, we were able to establish the likely pathomechanism for p.A789V: a disrupted hydrophobic pocket in the Sec7 domain structure, leading to loss of IQSEC2 ArfGEF activity

Summary

Introduction

Intellectual disability (ID) is a developmental brain disorder characterized by impaired intellectual and adaptive functions, and can be defined by an IQ below 70 and limitations in intellectual functioning and adaptive behaviors. As a result of the excess in males affected by ID, and the identification of families where ID shows clear X-linked segregation, significant attention has focused on the genetics of X-linked intellectual disability (XLID)—a common, clinically and genetically complex disorder often arising from mutations in one of >100 genes on the X chromosome. Recent studies questioned the implication of AGTR2, MAGT1, ZNF674, SRPX2, ATP6AP2, ARHGEF6, NXF5, ZCCHC12, ZNF41, ZNF81 and RAB40AL in XLID (Piton et al, 2013; Ołdak et al, 2014). This highlights the vital importance of structure-function analyses for validating potentially diseasecausing variants

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