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Prevalence of SHANK3 variants in patients with different subtypes of autism spectrum disorders
Open accessAbstract
Autism spectrum disorders (ASDs) include three main conditions: autistic disorder (AD), pervasive developmental disorder, not otherwise specified (PDD-NOS), and Asperger syndrome. It has been shown that many genes associated with ASDs are involved in the neuroligin-neurexin interaction at the glutamate synapse: NLGN3, NLGN4, NRXN1, CNTNAP2, and SHANK3. We screened this last gene in two cohorts of ASD patients (133 patients from US and 88 from Italy). We found 5/221 (2.3%) cases with pathogenic alterations: a 106 kb deletion encompassing the SHANK3 gene, two frameshift mutations leading to premature stop codons, a missense mutation (p.Pro141Ala), and a splicing mutation (c.1820-4 G>A). Additionally, in 17 patients (7.7%) we detected a c.1304+48C>T transition affecting a methylated cytosine in a CpG island. This variant is reported as SNP rs76224556 and was found in both US and Italian controls, but it results significantly more frequent in our cases than in the control cohorts. The variant is also significantly more common among PDD-NOS cases than in AD cases. We also screened this gene in an independent replication cohort of 104 US patients with ASDs, in which we found a missense mutation (p.Ala1468Ser) in 1 patient (0.9%), and in 8 patients (7.7%) we detected the c.1304+48C>T transition. While SHANK3 variants are present in any ASD subtype, the SNP rs76224556 appears to be significantly associated with PDD-NOS cases. This represents the first evidence of a genotype-phenotype correlation in ASDs and highlights the importance of a detailed clinical-neuropsychiatric evaluation for the effective genetic screening of ASD patients.
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“Similarly, in other cases with almost identical small microdeletions (<100 kb) including SHANK3, neurobehavioral phenotypes were quite variable (Boccuto et al., 2013; Bonaglia et al., 2011; Dhar et al., 2010).”
From Modeling Autism by SHANK Gene Mutations in Mice (2013) · cites this paper as Boccuto et al., 2013
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1 retracted
RETRACTED: Enhanced Polyubiquitination of Shank3 and NMDA Receptor in a Mouse Model of Autism
Bangash, M. A., Park, J. M., Melnikova, T., Wang, D., Jeon, S. K., Lee, D., Syeda, S. K., Kim, J., Kouser, M., Schwartz, J. L., et al. (2011) · Cell · doi:10.1016/j.cell.2011.03.052 · Cited by 116
RetractedStrong association of de novo copy number mutations with autism
Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., et al. (2007) · Science · doi:10.1126/science.1138659 · Cited by 2,795
Autism as a strongly genetic disorder: evidence from a British twin study
Bailey, A., Le Couteur, A., Gottesman, I., Bolton, P., Simonoff, E., Yuzda, E., & Rutter, M. (1995) · Psychological Medicine · doi:10.1017/s0033291700028099 · Cited by 2,461
McDonald-McGinn, D. M., Sullivan, K. E., Marino, B., Philip, N., Swillen, A., Vorstman, J. A. S., Zackai, E. H., Emanuel, B. S., Vermeesch, J. R., Morrow, B. E., et al. (2015) · Nature Reviews Disease Primers · doi:10.1038/nrdp.2015.71 · Cited by 2,236
Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism
Study, P. A. R. I. S., Jamain, S., Quach, H., Betancur, C., Råstam, M., Colineaux, C., Gillberg, I. C., Soderstrom, H., Giros, B., Leboyer, M., et al. (2003) · Nature Genetics · doi:10.1038/ng1136 · Cited by 1,851
Structural Variation of Chromosomes in Autism Spectrum Disorder
Marshall, C. R., Noor, A., Vincent, J. B., Lionel, A. C., Feuk, L., Skaug, J., Shago, M., Moessner, R., Pinto, D., Ren, Y., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.12.009 · Cited by 1,815
Conserved role of intragenic DNA methylation in regulating alternative promoters
Maunakea, A. K., Nagarajan, R. P., Bilenky, M., Ballinger, T. J., D’Souza, C., Fouse, S. D., Johnson, B. E., Hong, C., Nielsen, C., Zhao, Y., et al. (2010) · Nature · doi:10.1038/nature09165 · Cited by 1,743
Durand, C. M., Betancur, C., Boeckers, T. M., Bockmann, J., Chaste, P., Fauchereau, F., Nygren, G., Rastam, M., Gillberg, I. C., Anckarsäter, H., et al. (2007) · Nature Genetics · doi:10.1038/ng1933 · Cited by 1,602
Shank3 mutant mice display autistic-like behaviours and striatal dysfunction
Peça, J., Feliciano, C., Ting, J. T., Wang, W., Wells, M. F., Venkatraman, T. N., Lascola, C. D., Fu, Z., & Feng, G. (2011) · Nature · doi:10.1038/nature09965 · Cited by 1,570
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SHANK proteins: roles at the synapse and in autism spectrum disorder
Monteiro, P., & Feng, G. (2017) · Nature Reviews Neuroscience · doi:10.1038/nrn.2016.183 · Cited by 681
Leblond, C. S., Nava, C., Polge, A., Gauthier, J., Huguet, G., Lumbroso, S., Giuliano, F., Stordeur, C., Depienne, C., Mouzat, K., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004580 · Cited by 630
“To avoid population stratification bias in the calculation of the odds ratio (OR), studies without a control group were excluded (i.e. Boccuto et al. 2012 and Bremer et al. 2012) (Figure 2, 3, and Table 1).”
BackgroundMethodInfluentialModeling Autism by SHANK Gene Mutations in Mice
Jiang, Y.-H., & Ehlers, M. D. (2013) · Neuron · doi:10.1016/j.neuron.2013.03.016 · Cited by 488
SHANK3 and IGF1 restore synaptic deficits in neurons from 22q13 deletion syndrome patients
Shcheglovitov, A., Shcheglovitova, O., Yazawa, M., Portmann, T., Shu, R., Sebastiano, V., Krawisz, A., Froehlich, W., Bernstein, J. A., Hallmayer, J. F., et al. (2013) · Nature · doi:10.1038/nature12618 · Cited by 470
Soorya, L. V., Kolevzon, A. L., Zweifach, J., Lim, T., Dobry, Y., Schwartz, L., Frank, Y., Wang, A. T., Cai, G., Parkhomenko, E., et al. (2013) · Molecular Autism · doi:10.1186/2040-2392-4-18 · Cited by 345
Metadata
- Authors
- Boccuto, L., Lauri, M., Sarasua, S. M., Skinner, C. D., Buccella, D., Dwivedi, A., Orteschi, D., Collins, J. S., Zollino, M., Visconti, P., DuPont, B., Tiziano, D., Schroer, R. J., Neri, G., Stevenson, R. E., Gurrieri, F., & Schwartz, C. E.
- Affiliations
- Greenwood Genetic Center (US)
- Università Cattolica del Sacro Cuore (IT)
- Ospedale Maggiore Carlo Alberto Pizzardi (IT)
- Corresponding author
- Schwartz, Charles E
- ORCID
- Venue
- European Journal of Human Genetics
- Published
- 2012-08-15
- Volume
- 21
- Issue
- 3
- Pages
- 310-316
- ISSN
- 1018-4813 (ISSN-L)
- 1476-5438
- PMC
- PMC3573207
- OpenAlex
- W2016364319
- Cited by
- 240
- References
- 51
- Citations by year
- 2026: 7 · 2025: 13 · 2024: 20 · 2023: 21 · 2022: 18 · 2021: 21 · 2020: 22 · 2019: 13 · 2018: 23 · 2017: 16 · 2016: 13 · 2015: 18 · 2014: 21 · 2013: 14
- FWCI
- 8.69
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- European Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5r01hd026202-15)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01-HD026202, HD 26202)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- SHANK3, autism spectrum disorder, pervasive developmental disorder not otherwise specified, autistic disorder, Asperger syndrome, genotype-phenotype correlation, frameshift mutation, missense mutations, splicing mutation, CpG island methylation, genetic screening
- MeSH terms
- Child, Child Development Disorders, Pervasive, Cytosine, Female, Humans, Italy, Male, Mutation, Nerve Tissue Proteins, South Carolina, Cohort Studies, Gene Deletion, CpG Islands, Polymorphism, Single Nucleotide, Asperger Syndrome, Genetic Association Studies
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