No Association Between SRGAP3/MEGAP Haploinsufficiency and Mental Retardation

Mental retardation (MR) affects 2% to 3% of children and is defined by the presence of significant limitations in cognitive and adaptive behavior.¹ A classic neuropathological feature of patients with MR is altered dendritic spine morphology and/or density. These structural abnormalities reflect impaired cytoskeleton remodeling and are associated with synaptic dysfunction.² Members of the Rho family of guanosine triphosphateses (Rho GTPases) regulate cytoskeletal remodeling in the context of dendritic structures and synaptic plasticity. Mutations in several genes of the Rho-GTPase signaling pathway have been reported in MR.³ One example of such genes is SRGAP3/MEGAP, which encodes a Rho-GTPase activator (RhoGAP) that regulates actin remodeling.^4,5 The SRGAP3 gene was disrupted by a de novo balanced translocation in a patient with facial dysmorphism, hypotonia, and severe MR, features characteristic of 3p− microdeletion syndrome.⁴ The breakpoint was located between exons 3 and 4 of SRGAP3, and the translocation did not seem to be associated with copy number changes. SRGAP3 was also found to be among the genes deleted in some patients with 3p− microdeletion syndrome.⁴ Together, these observations suggest that SRGAP3 haploinsufficiency causes MR.

As part of the Synapse-to-Disease project aimed at performing large-scale mutation analysis of genes affecting the synapse in neurodevelopmental diseases, we sequenced SRGAP3 in patients with idiopathic MR (n = 95) or autism spectrum disorders (ASD; n = 142). Our findings suggest that heterozygous disruption of SRGAP3 is not associated with MR.

Cohorts of 95 sporadic cases of MR (without growth abnormalities or dysmorphic features), 142 patients with ASD, and 285 healthy ethnically matched individuals were recruited. Most individuals with MR or ASD and control individuals were French Canadian. After approval by the institutional ethics committees, blood samples were collected from all individuals and from their parents for genomic DNA extraction (Puregene DNA kit; Qiagen, Mississauga, Ontario, Canada). Paternity and maternity of all families were confirmed using 6 microsatellite markers. Twenty-two coding exons and their intronic flanking regions from SRGAP3 (chr3:8997278-9266311; RefSeq NM_014850) were amplified by polymerase chain reaction from genomic DNA and directly sequenced. Mutations were confirmed by reamplification and resequencing of the proband and the parents in both directions.

We identified the following 5 heterozygous missense mutations in SRGAP3: p.E394V (c.1181A>T; ASD:1/142), p.F511L (c.1531T>C; ASD:2/142), p.I628V (c.1882A>G; MR:1/95; ASD:1/142; dbSNP:rs2271207), p.V799I (c.2395G>A; MR:1/95), and p.G942C (c.2824G>T; ASD:1/142) (Figure). These mutations are predicted not to affect protein function⁶ and are unlikely to be pathogenic, as they are transmitted from healthy parents. We also identified one heterozygous nonsense mutation (c.1162C>T; p.Q388X) in a different patient with MR. This mutation lies in exon 8, before the alternatively spliced exon 12, and is predicted to truncate SRGAP3 upstream of its RhoGAP domain⁴; thus, it is expected to abolish SRGAP3 function (Figure). The proband with p.Q388X is an 18-year-old French Canadian woman with mild nonsyndromic MR. The heterozygous p.Q388X was also found in the DNA of the proband's mother, maternal uncle, and maternal grandfather, who are all healthy and display no cognitive deficits. This mutation was absent from the proband's healthy father and brother, from her sister who also shows mild nonsyndromic MR, and from 285 ethnically matched controls.

Here we describe a heterozygous SRGAP3-truncating mutation in 3 healthy individuals and 1 patient with MR, all from the same family. This finding and the fact that p.Q388X was found only in 1 of 2 sisters sharing a similar MR phenotype argue against the notion that heterozygous disruption of SRGAP3 causes MR. The previously described association between SRGAP3 and MR mainly relied on the observation of a balanced translocation disrupting this gene in a patient with MR.⁴ Balanced translocations are complex rearrangements that can cause disease through gain- and/or loss-of-function mechanisms. It remains unknown whether this translocation is coincidental in this patient, whether it causes MR by disrupting the expression of another gene, or whether it induces a gain-of-function effect that could involve SRGAP3.

Correspondence: Dr Michaud, Research Center, Centre Hospitalier Iniversitaire Sainte-Justine, 3175 Côte Sainte-Catherine, Montreal, Quebec, Canada H3T 1C5 (jacques.michaud@recherche-ste-justine.qc.ca).

Author Contributions:Study concept and design: Hamdan, Gauthier, Marineau, Lafrenière, Drapeau, Lacaille, Rouleau, and Michaud. Acquisition of data: Pellerin, Dobrzeniecka, Fombonne, and Mottron. Analysis and interpretation of data: Hamdan and Dobrzeniecka. Drafting of the manuscript: Hamdan and Michaud. Critical revision of the manuscript for important intellectual content: Gauthier, Pellerin, Dobrzeniecka, Marineau, Fombonne, Mottron, Lafrenière, Drapeau, Lacaille, and Rouleau. Obtained funding: Drapeau, Lacaille, Rouleau, and Michaud. Administrative, technical, and material support: Pellerin, Dobrzeniecka, Marineau, Fombonne, and Mottron. Study supervision: Hamdan, Gauthier, Lafrenière, Rouleau, and Michaud.

Financial Disclosure: None reported.

Funding/Support: This study was supported by the Canadian Institute of Health Research (CIHR) (Drs Rouleau, Lacaille, and Michaud); Fonds de la Recherche en Santé (FRSQ) (Dr Michaud); Genome Canada; Genome Quebec; and Université de Montréal for the Synapse-to-Disease (S2D) project (Drs Drapeau and Rouleau).

Additional Contributions: Synapse-to-Disease team, including the bioinformatic (Yan Yang, Dan Spiegelman, Mélanie Côté, and Ousmane Diallo) and genetic screening and polymerase chain reaction divisions (Sandra Laurent, Anne Noreau, Frédéric Kuku, Joannie Duguay, Laurie Destroismaisons, Karine Lachapelle, Philippe Jolivet, Pascale Thibodeau, and Annie Raymond); DNA extraction and paternity testing, Annie Levert and Judith St-Onge; DNA sequencing and analyses at the McGill University and Génome Québec Innovation Centre, Pierre Lepage, Sébastien Brunet, Hao Fan Yam, Louis Létourneau, and Louis Dumond Joseph.