Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein
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Abstract
PURPOSE: Although haploinsufficiency of ANKRD11 is among the most common genetic causes of neurodevelopmental disorders, the role of rare ANKRD11 missense variation remains unclear. We characterized clinical, molecular, and functional spectra of ANKRD11 missense variants. METHODS: We collected clinical information of individuals with ANKRD11 missense variants and evaluated phenotypic fit to KBG syndrome. We assessed pathogenicity of variants through in silico analyses and cell-based experiments. RESULTS: We identified 20 unique, mostly de novo, ANKRD11 missense variants in 29 individuals, presenting with syndromic neurodevelopmental disorders similar to KBG syndrome caused by ANKRD11 protein truncating variants or 16q24.3 microdeletions. Missense variants significantly clustered in repression domain 2 at the ANKRD11 C-terminus. Of the 10 functionally studied missense variants, 6 reduced ANKRD11 stability. One variant caused decreased proteasome degradation and loss of ANKRD11 transcriptional activity. CONCLUSION: Our study indicates that pathogenic heterozygous ANKRD11 missense variants cause the clinically recognizable KBG syndrome. Disrupted transrepression capacity and reduced protein stability each independently lead to ANKRD11 loss-of-function, consistent with haploinsufficiency. This highlights the diagnostic relevance of ANKRD11 missense variants, but also poses diagnostic challenges because the KBG-associated phenotype may be mild and inherited pathogenic ANKRD11 (missense) variants are increasingly observed, warranting stringent variant classification and careful phenotyping.
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- Authors
- de Boer, E., Ockeloen, C. W., Kampen, R. A., Hampstead, J. E., Dingemans, A. J. M., Rots, D., Lütje, L., Ashraf, T., Baker, R., Barat-Houari, M., Angle, B., Chatron, N., Denommé-Pichon, A.-S., Devinsky, O., Dubourg, C., Elmslie, F., Elloumi, H. Z., Faivre, L., Fitzgerald-Butt, S., Geneviève, D., Goos, J. A. C., Helm, B. M., Kini, U., Lasa-Aranzasti, A., Lesca, G., Lynch, S. A., Mathijssen, I. M. J., McGowan, R., Monaghan, K. G., Odent, S., Pfundt, R., Putoux, A., van Reeuwijk, J., Santen, G. W. E., Sasaki, E., Sorlin, A., van der Spek, P. J., Stegmann, A. P. A., Swagemakers, S. M. A., Valenzuela, I., Viora-Dupont, E., Vitobello, A., Ware, S. M., Wéber, M., Gilissen, C., Low, K. J., Fisher, S. E., Vissers, L. E. L. M., Wong, M. M. K., & Kleefstra, T.
- Affiliations
- Radboud University Nijmegen (NL)
- Max Planck Institute for Psycholinguistics (NL)
- Guy's Hospital (GB)
- Advocate Children's Hospital (US)
- Lyon 1 Université (FR)
- Centre National de la Recherche Scientifique (FR)
- University of London (GB)
- St George's, University of London (GB)
- Inserm (FR)
- Erasmus MC (NL)
- University of Oxford (GB)
- Children's Health Ireland at Crumlin (IE)
- Centre Hospitalier Universitaire de Rennes (FR)
- Maastricht University Medical Centre (NL)
- Vall d'Hebron Institut de Recerca (ES)
- University Hospitals Bristol and Weston NHS Foundation Trust (GB)
- Corresponding author
- Ockeloen, Charlotte W.
- ORCID
- de Boer, Elke
- Ockeloen, Charlotte W.
- Kampen, Rosalie A.
- Hampstead, Juliet E.
- Dingemans, Alexander J.M.
- Rots, Dmitrijs
- Ashraf, Tazeen
- Chatron, Nicolas
- Devinsky, Orrin
- Dubourg, Christèle
- Elmslie, Frances
- Faivre, Laurence
- Geneviève, David
- Helm, Benjamin M.
- Mathijssen, Irene M.J.
- McGowan, Ruth
- Odent, Sylvie
- Pfundt, Rolph
- Putoux, Audrey
- Santen, Gijs W.E.
- Sasaki, Erina
- Sorlin, Arthur
- Stegmann, Alexander P.A.
- Valenzuela, Irene
- Vitobello, Antonio
- Ware, Stephanie M.
- Gilissen, Christian
- Low, Karen J.
- Fisher, Simon E.
- Vissers, Lisenka E.L.M.
- Wong, Maggie M.K.
- Kleefstra, Tjitske
- Venue
- Genetics in Medicine
- Publisher
- Elsevier BV
- Published
- 2022-10
- Volume
- 24
- Issue
- 10
- Pages
- 2051-2064
- ISSN
- 1098-3600 (ISSN-L)
- OpenAlex
- W4285401205
- Cited by
- 28
- References
- 41
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 8 · 2023: 8 · 2022: 3
- FWCI
- 3.62
- Type
- journal article
- Language
- en
- Update notices
- erratum (2023-11-01)
- Open access
- hybrid
- doi.org
- Locations
- Genetics in Medicine (publishedVersion, cc-by)
- medRxiv (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion, cc-by)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion, cc-by)
- St George's Online Research Archive (St George's University of London) (acceptedVersion)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by)
- HAL (submittedVersion, cc-by)
- Leiden Repository (Leiden University) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- HAL (submittedVersion, other-oa)
- Explore Bristol Research (submittedVersion, cc-by)
- Purdue University Indianapolis (Indiana University) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion, other-oa)
- Research Publications (Maastricht University) (submittedVersion, other-oa)
- Funders
- Scottish Government
- European Commission (HICF-1009-003, HORIZON2020, 779257)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (015014066, 015.014.036, 91718310)
- Max-Planck-Gesellschaft
- Chief Scientist Office, Scottish Government Health and Social Care Directorate (SGP/1)
- Medical Research Council (MC_PC_15080)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- ANKRD11, KBG syndrome, missense mutations, haploinsufficiency, neurodevelopmental disorders, protein stability, proteasomal degradation, transcriptional activity, loss of function, variant interpretation, de novo mutations
- MeSH terms
- Abnormalities, Multiple, Bone Diseases, Developmental, Chromosome Deletion, Humans, Intellectual Disability, Phenotype, Repressor Proteins, Tooth Abnormalities, Transcription Factors, Facies, Mutation, Missense, Proteasome Endopeptidase Complex
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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