Cited by 424Genomic variations and chromosomal abnormalitiesGenetics and Neurodevelopmental DisordersGenome Rearrangement Algorithms

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KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant

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Golzio, Christelle, Willer, Jason, Talkowski, Michael E., Oh, Edwin C., Taniguchi, Yu, Jacquemont, Sébastien, Reymond, Alexandre, Sun, Mei, Sawa, Akira, Gusella, James F., Kamiya, Atsushi, Beckmann, Jacques S., Katsanis, Nicholas·2012·Nature

DOI 10.1038/nature11091PMC PMC3366115

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Abstract

Copy number variants (CNVs) are major contributors to genetic disorders. We have dissected a region of the 16p11.2 chromosome--which encompasses 29 genes--that confers susceptibility to neurocognitive defects when deleted or duplicated. Overexpression of each human transcript in zebrafish embryos identified KCTD13 as the sole message capable of inducing the microcephaly phenotype associated with the 16p11.2 duplication, whereas suppression of the same locus yielded the macrocephalic phenotype associated with the 16p11.2 deletion, capturing the mirror phenotypes of humans. Analyses of zebrafish and mouse embryos suggest that microcephaly is caused by decreased proliferation of neuronal progenitors with concomitant increase in apoptosis in the developing brain, whereas macrocephaly arises by increased proliferation and no changes in apoptosis. A role for KCTD13 dosage changes is consistent with autism in both a recently reported family with a reduced 16p11.2 deletion and a subject reported here with a complex 16p11.2 rearrangement involving de novo structural alteration of KCTD13. Our data suggest that KCTD13 is a major driver for the neurodevelopmental phenotypes associated with the 16p11.2 CNV, reinforce the idea that one or a small number of transcripts within a CNV can underpin clinical phenotypes, and offer an efficient route to identifying dosage-sensitive loci.

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Additional file 5 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
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Additional file 11 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X. Y., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907188
Additional file 10 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X. Y., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907185
Additional file 8 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X. Y., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907215
Additional file 1 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X. Y., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907194
Additional file 7 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X. Y., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907212
Additional file 2 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X. Y., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907197
Additional file 9 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X. Y., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907218
Etiology and Translational Research in Neurodevelopmental Disorders
Li, F., Xu, M., Yu, J., & Cao, M. Y. (2024) · Springer eBooks · doi:10.1007/978-981-97-7433-3_2
EGR3 Deletion Rescues Developmental and Epileptic Encephalopathy in Kcna1 -null MicePreprint
Mazumder, A. G., Karedia, S., Adhyapak, N., Schimer, C., Bass, J. S., Kamen, J. L., Jankovic, M. J., Miao, Q., Gallitano, A. L., Saltzman, A. B., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.07.658422
Bi-allelic mutations in KCTD11 cause a new form of autosomal recessive intermediate Charcot-Marie-Tooth diseasePreprint
Gadacha, J., Haidar, Z., Roëckel, N., Pauset, A., Castro, C., Provost, C., Hamzé, Z., Humbert, C., Bertaux, K., Lenfant, N., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.30.661538
Childhood obesity influences mid-to-late life bone health through shared genetic architecture
Xia, M., Qu, Y., Lei, B., Zhong, Y., Han, T., Sha, L., Zhu, J., Song, X., Yang, B. T., Deng, Q., et al. (2025) · Bone · doi:10.1016/j.bone.2025.117639
Inhibition of the neurodevelopmental disorder-associated 16p11.2 gene QPRT leads to altered cell type distribution in human stem cell-derived cerebral organoidsPreprint
Schwarzpaul, J., Droell, C. M., Kumar, A., Sarma, H., Gruenauer, M., Ucar, S. Z., Hechavarría, J. C., Chiocchetti, A. G., & Haslinger, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.08.673916
Genetics of Autism Spectrum Disorders: The Opportunity and Challenge in the Genetics Clinic
Wang, Y., Wang, P., Xu, X., Goldstein, J., McConkie‐Rosell, A., Cheung, S. W., & Jiang, Y. (2015) · Contemporary clinical neuroscience · doi:10.1007/978-1-4939-2190-4_4
Additional file 1 of Identifying foetal forebrain interneurons as a target for monogenic autism risk factors and the polygenic 16p11.2 microdeletion
Yang, Y., Booker, S. A., Clegg, J. M., Urzainqui, I. Q., Sumera, A., Kozić, Z., Dando, O., Lorenzo, S. M., Hérault, Y., Kind, P. C., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26562655
Additional file 5 of Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Kretz, P. F., Wagner, C., Mikhaleva, A., Montillot, C., Hugel, S., Morella, I., Kannan, M., Fischer, M., Milhau, M., Yalçın, İ., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26640508
Self-citation
Additional file 13 of Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Kretz, P. F., Wagner, C., Mikhaleva, A., Montillot, C., Hugel, S., Morella, I., Kannan, M., Fischer, M., Milhau, M., Yalçın, İ., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26640532
Self-citation
Additional file 1 of Targeting the RHOA pathway improves learning and memory in adult Kctd13 and 16p11.2 deletion mouse models
Lorenzo, S. M., Nalesso, V., Chevalier, C., Birling, M., & Hérault, Y. (2021) · Figshare · doi:10.6084/m9.figshare.13565934
Additional file 7 of Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Kretz, P. F., Wagner, C., Mikhaleva, A., Montillot, C., Hugel, S., Morella, I., Kannan, M., Fischer, M., Milhau, M., Yalçın, İ., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26640514
Self-citation
Additional file 9 of Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Kretz, P. F., Wagner, C., Mikhaleva, A., Montillot, C., Hugel, S., Morella, I., Kannan, M., Fischer, M., Milhau, M., Yalçın, İ., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26640520
Self-citation
Additional file 3 of Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Kretz, P. F., Wagner, C., Mikhaleva, A., Montillot, C., Hugel, S., Morella, I., Kannan, M., Fischer, M., Milhau, M., Yalçın, İ., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26640502
Self-citation
Additional file 1 of Three case reports of patients indicating the diversity of molecular and clinical features of 16p11.2 microdeletion anomaly
Szelest, M., Stefaniak, M., Ręka, G., Jaszczuk, I., & Lejman, M. (2021) · Figshare · doi:10.6084/m9.figshare.14196438
Additional file 2 of Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Kretz, P. F., Wagner, C., Mikhaleva, A., Montillot, C., Hugel, S., Morella, I., Kannan, M., Fischer, M., Milhau, M., Yalçın, İ., et al. (2024) · Figshare · doi:10.6084/m9.figshare.24572204
Self-citation
Additional file 6 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907209
Additional file 12 of Dissecting the autism-associated 16p11.2 locus identifies multiple drivers in neuroanatomical phenotypes and unveils a male-specific role for the major vault protein
Kretz, P. F., Wagner, C., Mikhaleva, A., Montillot, C., Hugel, S., Morella, I., Kannan, M., Fischer, M., Milhau, M., Yalçın, İ., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26640529
Self-citation
Additional file 12 of Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes
Vysotskiy, M., Zhong, X., Miller‐Fleming, T. W., Zhou, D., Cox, N. J., & Weiss, L. A. (2021) · Figshare · doi:10.6084/m9.figshare.16907191

Authors: Golzio, C., Willer, J., Talkowski, M. E., Oh, E. C., Taniguchi, Y., Jacquemont, S., Reymond, A., Sun, M., Sawa, A., Gusella, J. F., Kamiya, A., Beckmann, J. S., & Katsanis, N.
Affiliations: Duke University (US)
Harvard University (US)
Johns Hopkins University (US)
Centre Hospitalier Universitaire Vaudois (CH)
University of Lausanne (CH)
Massachusetts General Hospital (US)
Corresponding author: Katsanis, Nicholas
ORCID: Golzio, Christelle
Willer, Jason
Talkowski, Michael E.
Oh, Edwin C.
Jacquemont, Sébastien
Reymond, Alexandre
Sun, Mei
Sawa, Akira
Gusella, James F.
Kamiya, Atsushi
Beckmann, Jacques S.
Katsanis, Nicholas
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2012-05
Volume: 485
Issue: 7398
Pages: 363-367
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature11091
PMC: PMC3366115
OpenAlex: W1981693548
Cited by: 410
References: 33
Citations by year: 2026: 14 · 2025: 15 · 2024: 29 · 2023: 32 · 2022: 17 · 2021: 36 · 2020: 24 · 2019: 29 · 2018: 34 · 2017: 33 · 2016: 31 · 2015: 37 · 2014: 31 · 2013: 36 · 2012: 12
FWCI: 22.29
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
SERVAL (Université de Lausanne) (acceptedVersion, other-oa)
IRIS (submittedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
RePEc: Research Papers in Economics (submittedVersion)
Funders: National Science Foundation
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Fondation Leenaards
Université de Lausanne
National Institutes of Health (MH084018)
National Institute of Mental Health (MH-091230, R01MH091230, MH084018, P20MH084018, F32MH087123, P50MH094268, R01MH092443)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD06286)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords: microcephaly, macrocephaly, brain development, neuronal progenitor proliferation, apoptosis, autism spectrum disorder, schizophrenia, obesity, neuroanatomical phenotypes, genetic disorders
MeSH terms: Animals, Chromosomes, Human, Pair 16, Head, Humans, Microcephaly, Nuclear Proteins, Organ Size, Phenotype, RNA, Messenger, Transcription, Genetic, Zebrafish, Up-Regulation, Apoptosis, Sequence Deletion, Gene Dosage, Gene Duplication, Cell Proliferation, Mice, DNA Copy Number Variations

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KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant

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