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Cited by 419Genetics and Neurodevelopmental DisordersGenomics and Rare DiseasesGenomic variations and chromosomal abnormalities

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De Novo Mutations in Moderate or Severe Intellectual Disability

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Hamdan, Fadi F., Srour, Myriam, Capo-Chichi, Jose-Mario, Daoud, Hussein, Nassif, Christina, Patry, Lysanne, Massicotte, Christine, Ambalavanan, Amirthagowri, Spiegelman, Dan, Diallo, Ousmane, Henrion, Edouard, Dionne-Laporte, Alexandre, Fougerat, Anne, Pshezhetsky, Alexey V., Venkateswaran, Sunita, Rouleau, Guy A., Michaud, Jacques L.·2014·PLoS Genetics
DOI 10.1371/journal.pgen.1004772PMC PMC4214635
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Abstract

Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID.

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Figure 1 Number of DNMs per affected individual in each trio.
Figure 1 Number of DNMs per affected individual in each trio.CC BY · PubMed Central
Figure 2 Physical protein-protein interaction network generated by GeneMANIA (http://www.GeneMANIA.org/; Gene Ontology molecular function based weighting). The Query genes included those listed in Table 3 from this study (in bold) and known and candidate ID genes reported with predicted-damaging DNMs from other studies (Table S2). Known ID genes are in red. The resulting network of 38 interconnected proteins was found to be enriched for proteins whose Gene Ontology molecular functions are implicated in the glutamate receptor signalling pathway (GRIN1, GRIN2A, GRIN2B, GRIA1, CACNG2, SHANK3; FDR q-value = 7.04e-6).
Figure 2 Physical protein-protein interaction network generated by GeneMANIA (http://www.GeneMANIA.org/; Gene Ontology molecular function based weighting). The Query genes included those listed in Table 3 from this study (in bold) and known and candidate ID genes reported with predicted-damaging DNMs from other studies (Table S2). Known ID genes are in red. The resulting network of 38 interconnected proteins was found to be enriched for proteins whose Gene Ontology molecular functions are implicated in the glutamate receptor signalling pathway (GRIN1, GRIN2A, GRIN2B, GRIA1, CACNG2, SHANK3; FDR q-value = 7.04e-6).CC BY · PubMed Central

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Metadata

Authors
Hamdan, F. F., Srour, M., Capo-Chichi, J.-M., Daoud, H., Nassif, C., Patry, L., Massicotte, C., Ambalavanan, A., Spiegelman, D., Diallo, O., Henrion, E., Dionne-Laporte, A., Fougerat, A., Pshezhetsky, A. V., Venkateswaran, S., Rouleau, G. A., & Michaud, J. L.
Affiliations
  • CHU Sainte-Justine Research Center (CA)
  • Montreal Children's Hospital (CA)
  • Montreal Neurological Institute and Hospital (CA)
  • Children's Hospital of Eastern Ontario (CA)
Corresponding author
Michaud, Jacques L.
ORCID
Venue
PLoS Genetics
Publisher
Public Library of Science (PLoS)
Published
2014-10-30
Volume
10
Issue
10
Pages
e1004772
ISSN
  • 1553-7390 (ISSN-L)
  • 1553-7404
DOI
10.1371/journal.pgen.1004772
PMC
PMC4214635
OpenAlex
W2058423880
Cited by
419
References
62
Citations by year
2026: 18 · 2025: 27 · 2024: 23 · 2023: 27 · 2022: 39 · 2021: 45 · 2020: 33 · 2019: 43 · 2018: 52 · 2017: 49 · 2016: 43 · 2015: 20
FWCI
24.22
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • eScholarship@McGill (McGill) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
Funders
  • McGill University
  • Canadian Institutes of Health Research
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
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Keywords
de novo mutations, intellectual disability, exome sequencing, loss-of-function mutations, single nucleotide substitution, ARID1B, CHD2, FOXG1, GABRB3, NR2B subunit, MBD5, MED13L, SETBP1, Tbr1, TCF4, WDR45, protein network analysis, diagnostic yield, pathogenic variants
MeSH terms
Epilepsy, Humans, Intellectual Disability, RNA Splicing, Frameshift Mutation, Point Mutation, Sequence Deletion, Codon, Nonsense, Mutation, Missense, Exome

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