CDK19-related disorder results from both loss-of-function and gain-of-function de novo missense variants.
Journal
Genetics in medicine : official journal of the American College of Medical Genetics
ISSN: 1530-0366
Titre abrégé: Genet Med
Pays: United States
ID NLM: 9815831
Informations de publication
Date de publication:
06 2021
06 2021
Historique:
received:
19
08
2020
accepted:
22
12
2020
revised:
18
12
2020
pubmed:
27
1
2021
medline:
8
7
2021
entrez:
26
1
2021
Statut:
ppublish
Résumé
To expand the recent description of a new neurodevelopmental syndrome related to alterations in CDK19. Individuals were identified through international collaboration. Functional studies included autophosphorylation assays for CDK19 Gly28Arg and Tyr32His variants and in vivo zebrafish assays of the CDK19 We describe 11 unrelated individuals (age range: 9 months to 14 years) with de novo missense variants mapped to the kinase domain of CDK19, including two recurrent changes at residues Tyr32 and Gly28. In vitro autophosphorylation and substrate phosphorylation assays revealed that kinase activity of protein was lower for p.Gly28Arg and higher for p.Tyr32His substitutions compared with that of the wild-type protein. Injection of CDK19 messenger RNA (mRNA) with either the Tyr32His or the Gly28Arg variants using in vivo zebrafish model significantly increased fraction of embryos with morphological abnormalities. Overall, the phenotype of the now 14 individuals with CDK19-related disorder includes universal developmental delay and facial dysmorphism, hypotonia (79%), seizures (64%), ophthalmologic anomalies (64%), and autism/autistic traits (56%). CDK19 de novo missense variants are responsible for a novel neurodevelopmental disorder. Both kinase assay and zebrafish experiments showed that the pathogenetic mechanism may be more diverse than previously thought.
Identifiants
pubmed: 33495529
doi: 10.1038/s41436-020-01091-9
pii: S1098-3600(21)05205-9
doi:
Substances chimiques
CDK19 protein, human
EC 2.7.11.22
Cyclin-Dependent Kinases
EC 2.7.11.22
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1050-1057Subventions
Organisme : NCATS NIH HHS
ID : UL1 TR002538
Pays : United States
Références
Malumbres, M. Cyclin-dependent kinases. Genome Biol. 15, 122 (2014).
doi: 10.1186/gb4184
Spaeth, J. M., Kim, N. H. & Boyer, T. G. Mediator and human disease. Semin. Cell Dev. Biol. 22, 776–787 (2011).
doi: 10.1016/j.semcdb.2011.07.024
Calpena, E. et al. De novo missense substitutions in the gene encoding CDK8, a regulator of the mediator complex, cause a syndromic developmental disorder. Am. J. Hum. Genet. 104, 709–720 (2019).
doi: 10.1016/j.ajhg.2019.02.006
Nizon, M. et al. Variants in MED12L, encoding a subunit of the mediator kinase module, are responsible for intellectual disability associated with transcriptional defect. Genet. Med. 21, 2713–2722 (2019).
doi: 10.1038/s41436-019-0557-3
Furumoto, T. et al. A kinase subunit of the human mediator complex, CDK8, positively regulates transcriptional activation. Genes Cells 12, 119–132 (2007).
doi: 10.1111/j.1365-2443.2007.01036.x
Dannappel, M. V., Sooraj, D., Loh, J. J. & Firestein, R. Molecular and in vivo functions of the CDK8 and CDK19 kinase modules. Front. Cell. Dev. Biol. 6, 171 (2018).
doi: 10.3389/fcell.2018.00171
Allen, B. L. & Taatjes, D. J. The Mediator complex: a central integrator of transcription. Nat. Rev. Mol. Cell. Biol. 16, 155–166 (2015).
doi: 10.1038/nrm3951
Daniels, D. et al. Mutual exclusivity of MED12/MED12L, MED13/13L, and CDK8/19 paralogs revealed within the CDK-Mediator kinase module. J Proteomics Bioinform. S2:004. https://doi.org/10.4172/jpb.S2-004 .
Adegbola, A. et al. Redefining the MED13L syndrome. Eur J Hum. Genet. 23, 1308–1317 (2015).
doi: 10.1038/ejhg.2015.26
Graham, J. M. Jr. & Schwartz, C. E. MED12 related disorders. Am. J. Med. Genet. A. 161A, 2734–2740 (2013).
doi: 10.1002/ajmg.a.36183
Snijders Blok, L. et al. De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder. Hum. Genet. 137, 375–388 (2018).
doi: 10.1007/s00439-018-1887-y
Poot, M. Mutations in mediator complex genes CDK8, MED12, MED13, and MEDL13 mediate overlapping developmental syndromes. Mol. Syndromol. 10, 239–242 (2020).
doi: 10.1159/000502346
Poss, Z. C., Ebmeier, C. C. & Taatjes, D. J. The Mediator complex and transcription regulation. Crit. Rev. Biochem. Mol. Biol. 48, 575–608 (2013).
doi: 10.3109/10409238.2013.840259
Mukhopadhyay, A. et al. CDK19 is disrupted in a female patient with bilateral congenital retinal folds, microcephaly and mild mental retardation. Hum. Genet. 128, 281–291 (2010).
doi: 10.1007/s00439-010-0848-x
Chung, H. L. et al. De novo variants in CDK19 are associated with a syndrome involving intellectual disability and epileptic encephalopathy. Am. J. Hum. Genet. 106, 717–725 (2020).
doi: 10.1016/j.ajhg.2020.04.001
Li, J. et al. VarCards: an integrated genetic and clinical database for coding variants in the human genome. Nucleic Acids Res. 46, D1039–D1048 (2018).
doi: 10.1093/nar/gkx1039
Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17, 405–424 (2015).
doi: 10.1038/gim.2015.30
Venselaar, H., Te Beek, T. A., Kuipers, R. K., Hekkelman, M. L. & Vriend, G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics 11, 548 (2010).
doi: 10.1186/1471-2105-11-548
Capriotti, E., Fariselli, P. & Casadio, R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 33, W306–310 (2005).
doi: 10.1093/nar/gki375
Hirose, Y. & Manley, J. L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature. 395, 93–96 (1998).
doi: 10.1038/25786
Hirose, Y., Iwamoto, Y., Sakuraba, K., Yunokuchi, I., Harada, F. & Ohkuma, Y. Human phosphorylated CTD-interacting protein, PCIF1, negatively modulates gene expression by RNA polymerase II. Biochem. Biophys. Res. Commun. 369, 449–455 (2008).
doi: 10.1016/j.bbrc.2008.02.042
Sobreira, N., Schiettecatte, F., Valle, D. & Hamosh, A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum. Mutat. 36, 928–930 (2015).
doi: 10.1002/humu.22844
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 536, 285–291 (2016).
doi: 10.1038/nature19057
Niknafs, N. et al. MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures. Hum. Genet. 132, 1235–1243 (2013).
doi: 10.1007/s00439-013-1325-0
Tsutsui, T., Fukasawa, R., Tanaka, A., Hirose, Y. & Ohkuma, Y. Identification of target genes for the CDK subunits of the Mediator complex. Genes Cells 16, 1208–1218 (2011).
doi: 10.1111/j.1365-2443.2011.01565.x
Audetat, K. A., Galbraith, M.D., & Odell, A. T. et al. A kinase-independent role for cyclin-dependent kinase 19 in p53 response. Mol. Cell. Biol. 37, e00626-16 (2017).
Liu, W. et al. IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics. 31, 3359–3361 (2015).
doi: 10.1093/bioinformatics/btv362