Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features Article Swipe
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· 2024
· Open Access
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· DOI: https://doi.org/10.1016/j.xhgg.2024.100273
Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.xhgg.2024.100273
- OA Status
- gold
- Cited By
- 2
- References
- 84
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4391349613
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4391349613Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.xhgg.2024.100273Digital Object Identifier
- Title
-
Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental featuresWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
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2024-01-30Full publication date if available
- Authors
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Morad Ansari, Kamli N. W. Faour, Akiko Shimamura, Graeme R. Grimes, Emeline M. Kao, Erica R. Denhoff, Ana Blatnik, Daniel Ben-Isvy, Lily Wang, Benjamin M. Helm, Helen V. Firth, Amy M. Breman, Emilia K. Bijlsma, Aiko Iwata‐Otsubo, Thomy de Ravel, Vincent A. Fusaro, Alan Fryer, Keith Nykamp, Lara G. Stühn, Tobias B. Haack, G. Christoph Korenke, Panayiotis Constantinou, Kinga M. Bujakowska, Karen Low, Emily Place, Jennifer B. Humberson, Melanie P. Napier, Jessica F. Hoffman, Jane Juusola, Matthew A. Deardorff, Wanqing Shao, Shira Rockowitz, Ian D. Krantz, Maninder Kaur, Sarah E. Raible, Victoria Dortenzio, Sabine Kliesch, Moriel Singer‐Berk, Emily Groopman, Stephanie DiTroia, Sonia Ballal, Siddharth Srivastava, Kathrin Rothfelder, Saskia Biskup, Jessica Rzasa, Jennifer Kerkhof, Haley McConkey, Bekim Sadiković, Sarah K. Hilton, Siddharth Banka, Frank Tüttelmann, Donald F. Conrad, Anne O’Donnell‐Luria, Michael E. Talkowski, David Fitzpatrick, Philip M. BooneList of authors in order
- Landing page
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https://doi.org/10.1016/j.xhgg.2024.100273Publisher landing page
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://doi.org/10.1016/j.xhgg.2024.100273Direct OA link when available
- Concepts
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Biology, Missense mutation, Genetics, Loss function, Human genetics, Phenotype, Population, Indel, Intellectual disability, Gene, Single-nucleotide polymorphism, Genotype, Demography, SociologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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2Total citation count in OpenAlex
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2025: 1, 2024: 1Per-year citation counts (last 5 years)
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84Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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