Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability

Abstract

The first family identified as having a nonsyndromic intellectual disability was mapped in 1988. Here we show that a mutation of IQSEC2, encoding a guanine nucleotide exchange factor for the ADP-ribosylation factor family of small GTPases, caused this disorder. In addition to MRX1, IQSEC2 mutations were identified in three other families with X-linked intellectual disability. This discovery was made possible by systematic and unbiased X chromosome exome resequencing.

Figure 1

Identification of IQSEC2 mutations. cDNA (NM_001111125) and protein (NP_001104595) annotation of individual mutations is shown for each family. Pedigrees of MRX1 and MRX18 families have been updated since their last publication. Open symbols represent normal individuals, filled squares represent affected males, open circles with middle dots represent carrier females and cross-hatched squares represent males with learning problems but without an IQSEC2 mutation. Two carrier females with some learning problems from the MRX18 and AU128 families are shown with half the circle black. Individual generations are numbered with Roman numerals on the left of each pedigree. Individuals tested for the nucleotide substitution in each family are indicated either M (mutant allele) or M/N (mutant and normal allele). The genotypes of some females tested have not been shown due to privacy issues.

Figure 2

IQSEC2 structure and mutations. (a) Scheme of the human IQSEC2 protein (NP_001104595); shown are the IQ-like domain, Sec7 domain, pleckstrin homology domain (PH) and PDZ binding motif (UniprotKB/Swiss-Prot for Q5J85;1,488-amino-acid protein). Mutations in each family are shown above. (b) Missense mutations introduced into the Sec7 domain (light gray) diminish the GTP binding activity compared to the Sec7 wild-type (black) activity to levels seen with the E849A dominant negative mutant (dark gray) predicted to reduce GEF activity of the Sec7 domain. An all-groups comparison of the mean pMol of GTP bound to ARF6 was achieved by linear mixed model analysis. *P < 0.0001 compared to Sec7Wt. (c) Wild-type (Wt) ARF6-HA and Flag-tagged wild-type or mutant IQSEC2 were transfected into HEK293 cells and lysates were subjected to a pull-down assay with GST:GGA3 to isolate ARF6-GTP. The precipitates (above, top row) and lysates (above, bottom row) were probed with anti-HA to detect ARF6 and anti-Flag to detect expression of IQSEC2 (above, middle row). ARF6-GTP levels were normalized to total ARF6 levels and shown as the fold-increase over ARF6 transfected with empty vector. The E849K dominant negative mutation abolishes GEF activity of the Sec 7 domain. Data are mean ± s.e.m. from three independent experiments (bottom panel). (d) The IQ-like motif sequence lacks the G and second basic residue of the IQ motif. Characters within parentheses can substitute for each other. The R359C mutation disrupts the basic (R) residue (in bold and boxed).