Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability
Open accessAbstract
Little is known about the genetics of nonsyndromic intellectual disability (NSID). We hypothesized that de novo mutations (DNMs) in synaptic genes explain an important fraction of sporadic NSID cases. In order to investigate this possibility, we sequenced 197 genes encoding glutamate receptors and a large subset of their known interacting proteins in 95 sporadic cases of NSID. We found 11 DNMs, including ten potentially deleterious mutations (three nonsense, two splicing, one frameshift, four missense) and one neutral mutation (silent) in eight different genes. Calculation of point-substitution DNM rates per functional and neutral site showed significant excess of functional DNMs compared to neutral ones. De novo truncating and/or splicing mutations in SYNGAP1, STXBP1, and SHANK3 were found in six patients and are likely to be pathogenic. De novo missense mutations were found in KIF1A, GRIN1, CACNG2, and EPB41L1. Functional studies showed that all these missense mutations affect protein function in cell culture systems, suggesting that they may be pathogenic. Sequencing these four genes in 50 additional sporadic cases of NSID identified a second DNM in GRIN1 (c.1679_1681dup/p.Ser560dup). This mutation also affects protein function, consistent with structural predictions. None of these mutations or any other DNMs were identified in these genes in 285 healthy controls. This study highlights the importance of the glutamate receptor complexes in NSID and further supports the role of DNMs in this disorder.
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Δex4-9 and Δex4-7 mouse mutations are closest to patients with intragenic exon 1-9 deletion and splice mutation of intron 5 in SHANK3.
“The Δex4-9 (Bozdagi et al., 2010) and Δex4-7 mutations in mouse (Peca et al., 2011) are closest to patients with intragenic exon 1-9 deletion and splice mutation of intron 5 in SHANK3 (Bonaglia et al., 2011; Hamdan et al., 2011)”
From Modeling Autism by SHANK Gene Mutations in Mice (2013) · cites this paper as Hamdan et al., 2011
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- Authors
- Hamdan, F. F., Gauthier, J., Araki, Y., Lin, D.-T., Yoshizawa, Y., Higashi, K., Park, A.-R., Spiegelman, D., Dobrzeniecka, S., Piton, A., Tomitori, H., Daoud, H., Massicotte, C., Henrion, E., Diallo, O., Shekarabi, M., Marineau, C., Shevell, M., Maranda, B., Mitchell, G., Nadeau, A., D'Anjou, G., Vanasse, M., Srour, M., Lafrenière, R. G., Drapeau, P., Lacaille, J. C., Kim, E., Lee, J.-R., Igarashi, K., Huganir, R. L., Rouleau, G. A., & Michaud, J. L.
- Affiliations
- Centre Hospitalier Universitaire Sainte-Justine (CA)
- Centre Hospitalier de l’Université de Montréal (CA)
- Howard Hughes Medical Institute (US)
- Chiba University (JP)
- Korea Research Institute of Bioscience and Biotechnology (KR)
- Montreal Children's Hospital (CA)
- Centre hospitalier de l'Université Laval (CA)
- Université de Montréal (CA)
- Korea Advanced Institute of Science and Technology (KR)
- Corresponding author
- Michaud, Jacques L.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2011-03
- Volume
- 88
- Issue
- 3
- Pages
- 306-316
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC3059427
- OpenAlex
- W2033759150
- Cited by
- 349
- References
- 58
- Citations by year
- 2026: 8 · 2025: 14 · 2024: 15 · 2023: 19 · 2022: 16 · 2021: 20 · 2020: 24 · 2019: 24 · 2018: 21 · 2017: 37 · 2016: 18 · 2015: 38 · 2014: 30 · 2013: 19 · 2012: 31
- FWCI
- 18.96
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- KRIBB Repository (submittedVersion)
- Funders
- Canadian Institutes of Health Research
- Japan Society for the Promotion of Science (23390038)
- National Institute of Neurological Disorders and Stroke (R01NS036715)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Down syndrome and intellectual disability research
- Keywords
- non-syndromic intellectual disability, de novo mutations, glutamate receptors, glutamatergic synapses, synaptic genes, missense mutations, truncating mutations, splicing mutation, SYNGAP1, STXBP1, SHANK3, KIF1A, GRIN1, protein function
- MeSH terms
- Animals, Base Sequence, Cytoskeletal Proteins, Female, Humans, Male, Membrane Proteins, Intellectual Disability, Mutation, Neuropeptides, Phenotype, Protein Binding, RNA Splicing, Subcellular Fractions, Syndrome, Calcium Channels, Receptors, N-Methyl-D-Aspartate, Kinesins, Receptors, AMPA, Glutamic Acid, Amino Acid Substitution, Mutation, Missense, Protein Transport, Rats, HEK293 Cells
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