A novel splicing mutation in the IQSEC2 gene that modulates the phenotype severity in a family with intellectual disability

Abstract

The IQSEC2 gene is located on chromosome Xp11.22 and encodes a guanine nucleotide exchange factor for the ADP-ribosylation factor family of small GTPases. This gene is known to have a significant role in cytoskeletal organization, dendritic spine morphology and synaptic organization. Variants in IQSEC2 cause moderate to severe intellectual disability in males and a variable phenotype in females because this gene escapes from X-chromosome inactivation. Here we report on the first splicing variant in IQSEC2 (g.88032_88033del; NG_021296.1) that co-segregates in a family diagnosed with an X-linked form of ID. In a percentage of the cells, the variant activates an intraexonic splice acceptor site that abolishes 26 amino acids from the highly conserved PH domain of IQSEC2 and creates a premature stop codon 36 amino acids later in exon 13. Interestingly, the percentage of aberrant splicing seems to correlate with the severity of the disease in each patient. The impact of this variant in the target tissue is unknown, but we can hypothesize that these differences may be related to the amount of abnormal IQSEC2 transcript. To our knowledge, we are reporting a novel mechanism of IQSEC2 involvement in ID. Variants that affect splicing are related to many genetic diseases and the understanding of their role in disease expands potential opportunities for gene therapy. Modulation of aberrant splicing transcripts can become a potent therapeutic approach for many of these diseases.

Figure 1

Pedigree of the family. The individuals who could be tested are indicated as carrying the 2-bp deletion or not (wt). NA, not available; wt, wild type.

Figure 2

Images of four of the individuals carrying the mutation in the IQSEC2 gene. All present similar facial features with bulbous nose, smooth wide philtrum and thin upper lip. (a) Patient II5 at the age of 32 years. He presents with severe ID. (b) Patient II6 at the age of 29 years. He presents with moderate ID. (c) Patient II.4 at the age of 39 years. She presents with mild ID. (d) Patient I2 at the age of 62 years. She presented mild ID.

Figure 3

Analysis of IQSEC2 cDNA. The amplified products encompassing exons 10–13 are shown. (a) The first six bands correspond to mRNA IQSEC2 products obtained from lymphocytes. Two bands were visualized in mutation carrier samples, whereas only one band was visualized in samples from healthy relatives. The first column corresponds to 1 kb plus DNA ladder. Note the different intensity patterns of the bands in the patients. (b) Amplification pattern in mRNA from fibroblasts from patients I2 and II5. +C indicates pretreatment with cycloheximide.

Figure 4

The top panel (a) shows an IQSEC2 wild-type PCR product in which the normal exon structure from exons 10–13 is maintained. The bottom panel (b) shows the isolated 374-bp PCR product that corresponds to the aberrant spliced form in which 79 nucleotides of exon 12 are deleted. (c) The splicing patterns identified in the patients are represented schematically. Exons and introns are indicated by boxes and horizontal lines, respectively. The diagonal lines indicate the splicing events that were observed in lymphocytes and fibroblasts. The figure is not drawn to scale.