Expanding the Spectrum of KDM5C Neurodevelopmental Disorder: A Novel De Novo Stop Variant in a Young Woman and Emerging Genotype–Phenotype Correlations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genetic Analyses
2.2. Analysis of the X Chromosome Methylation Status
2.3. Retrospective Study
3. Results
3.1. Clinical Presentation of the Patient
3.2. Genetic Findings
3.3. Genotype–Phenotype Correlations
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Hatch, H.A.M.; O’Neil, M.H.; Marion, R.W.; Secombe, J.; Shulman, L.H. Caregiver-reported characteristics of children diagnosed with pathogenic variants in KDM5C. Am. J. Med. Genet. A 2021, 185, 2951–2958. [Google Scholar] [CrossRef]
- Hatch, H.A.M.; Secombe, J. Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. FEBS J. 2021. [Google Scholar] [CrossRef] [PubMed]
- Schenkel, L.C.; Aref-Eshghi, E.; Skinner, C.; Ainsworth, P.; Lin, H.; Paré, G.; Rodenhiser, D.I.; Schwartz, C.; Sadikovic, B. Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C. Clin. Epigenet. 2018, 10, 21. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Coursimault, J.; Goldenberg, A.; Nicolas, G.; Saugier-Veber, P.; Coutant, S.; Vincent, A.; Pouliquen, D.; Feltin, C.; Aref-Eshghi, E.; Sadikovic, B.; et al. Contribution of DNA methylation profiling to the reclassification of a variant of uncertain significance in the KDM5C gene. Eur. J. Med. Genet. 2022, 65, 104556. [Google Scholar] [CrossRef] [PubMed]
- Iwase, S.; Brookes, E.; Agarwal, S.; Badeaux, A.I.; Ito, H.; Vallianatos, C.N.; Tomassy, G.S.; Kasza, T.; Lin, G.; Thompson, A.; et al. A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation. Cell Rep. 2016, 14, 1000–1009. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Scandaglia, M.; Lopez-Atalaya, J.P.; Medrano-Fernandez, A.; Lopez-Cascales, M.T.; Del Blanco, B.; Lipinski, M.; Benito, E.; Olivares, R.; Iwase, S.; Shi, Y.; et al. Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons. Cell Rep. 2017, 21, 47–59. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Samanta, M.K.; Gayen, S.; Harris, C.; Maclary, E.; Murata-Nakamura, Y.; Malcore, R.M.; Porter, R.S.; Garay, P.M.; Vallianatos, C.N.; Samollow, P.B.; et al. Activation of Xist by an evolutionarily conserved function of KDM5C demethylase. Nat. Commun. 2022, 13, 2602. [Google Scholar] [CrossRef]
- Richards, S.; Aziz, N.; Bale, S.; Bick, D.; Das, S.; Gastier-Foster, J.; Grody, W.W.; Hegde, M.; Lyon, E.; Spector, E.; 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. 2015, 17, 405–424. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Elstein, D.; Schachamorov, E.; Beeri, R.; Altarescu, G. X-inactivation in Fabry disease. Gene 2012, 505, 266–268. [Google Scholar] [CrossRef] [PubMed]
- Warburton, D.; Kline, J.; Kinney, A.; Yu, C.Y.; Levin, B.; Brown, S. Skewed X chromosome inactivation and trisomic spontaneous abortion: No association. Am. J. Hum. Genet. 2009, 85, 179–193. [Google Scholar] [CrossRef]
- Jensen, L.R.; Amende, M.; Gurok, U.; Moser, B.; Gimmel, V.; Tzschach, A.; Janecke, A.R.; Tariverdian, G.; Chelly, J.; Fryns, J.P.; et al. Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am. J. Hum. Genet. 2005, 76, 227–236. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Santos, C.; Rodriguez-Revenga, L.; Madrigal, I.; Badenas, C.; Pineda, M.; Milà, M. A novel mutation in JARID1C gene associated with mental retardation. Eur. J. Hum. Genet. 2006, 14, 583–586. [Google Scholar] [CrossRef] [PubMed]
- Tzschach, A.; Lenzner, S.; Moser, B.; Reinhardt, R.; Chelly, J.; Fryns, J.P.; Kleefstra, T.; Raynaud, M.; Turner, G.; Ropers, H.H.; et al. Novel JARID1C/SMCX mutations in patients with X-linked mental retardation. Hum. Mutat. 2006, 27, 389. [Google Scholar] [CrossRef] [PubMed]
- Abidi, F.E.; Holloway, L.; Moore, C.A.; Weaver, D.D.; Simensen, R.J.; Stevenson, R.E.; Rogers, R.C.; Schwartz, C.E. Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia. J. Med. Genet. 2008, 45, 787–793. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rujirabanjerd, S.; Nelson, J.; Tarpey, P.S.; Hackett, A.; Edkins, S.; Raymond, F.L.; Schwartz, C.E.; Turner, G.; Iwase, S.; Shi, Y.; et al. Identification and characterization of two novel JARID1C mutations: Suggestion of an emerging genotype-phenotype correlation. Eur. J. Hum. Genet. 2010, 18, 330–335. [Google Scholar] [CrossRef] [Green Version]
- Santos-Rebouças, C.B.; Fintelman-Rodrigues, N.; Jensen, L.R.; Kuss, A.W.; Ribeiro, M.G.; Campos, M., Jr.; Santos, J.M.; Pimentel, M.M. A novel nonsense mutation in KDM5C/JARID1C gene causing intellectual disability, short stature and speech delay. Neurosci. Lett. 2011, 498, 67–71. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ounap, K.; Puusepp-Benazzouz, H.; Peters, M.; Vaher, U.; Rein, R.; Proos, A.; Field, M.; Reimand, T. A novel c.2T > C mutation of the KDM5C/JARID1C gene in one large family with X-linked intellectual disability. Eur. J. Med. Genet. 2012, 55, 178–184. [Google Scholar] [CrossRef] [PubMed]
- Guerra, J.V.S.; Oliveira-Santos, J.; Oliveira, D.F.; Leal, G.F.; Oliveira, J.R.M.; Costa, S.S.; Krepischi, A.C.V.; Vianna-Morgante, A.M.; Maschietto, M. DNA methylation fingerprint of monozygotic twins and their singleton sibling with intellectual disability carrying a novel KDM5C mutation. Eur. J. Med. Genet. 2020, 63, 103737. [Google Scholar] [CrossRef]
- Carmignac, V.; Nambot, S.; Lehalle, D.; Callier, P.; Moortgat, S.; Benoit, V.; Ghoumid, J.; Delobel, B.; Smol, T.; Thuillier, C.; et al. Further delineation of the female phenotype with KDM5C disease causing variants: 19 new individuals and review of the literature. Clin. Genet. 2020, 98, 43–55. [Google Scholar] [CrossRef] [PubMed]
- Lippa, N.C.; Barua, S.; Aggarwal, V.; Pereira, E.; Bain, J.M. A novel de novo KDM5C variant in a female with global developmental delay and ataxia: A case report. BMC Neurol. 2021, 21, 358. [Google Scholar] [CrossRef]
- Wu, P.M.; Yu, W.H.; Chiang, C.W.; Wu, C.Y.; Chen, J.S.; Tu, Y.F. Novel Variations in the KDM5C Gene Causing X-Linked Intellectual Disability. Neurol. Genet. 2021, 8, e646. [Google Scholar] [CrossRef] [PubMed]
- Lintas, C.; Sacco, R.; Azzarà, A.; Cassano, I.; Gurrieri, F. Genotype-Phenotype Correlations in Relation to Newly Emerging Monogenic Forms of Autism Spectrum Disorder and Associated Neurodevelopmental Disorders: The Importance of Phenotype Reevaluation after Pangenomic Results. J. Clin. Med. 2021, 10, 5060. [Google Scholar] [CrossRef] [PubMed]
- Brookes, E.; Laurent, B.; Õunap, K.; Carroll, R.; Moeschler, J.B.; Field, M.; Schwartz, C.E.; Gecz, J.; Shi, Y. Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity. Hum. Mol. Genet. 2015, 24, 2861–2872. [Google Scholar] [CrossRef] [PubMed]
Case | Fam No. | Familiar/De Novo | Mutation Type/Position | Detailed Clinical Features at Last Evaluation | Ref. |
---|---|---|---|---|---|
1 | 1 | de novo |
| Evaluated at 27 years
| Our case |
2 | 2 | de novo |
| Evaluated at 3 ys
| [20] |
3 | 3 | inherited |
| Evaluated at 18 ys
| [4] |
4 | 4 | not known, mother |
| Evaluated at 42 ys
| [17] |
5 | 4 | inherited, monozygous triplet |
| Evaluated at 16 ys
| [17] |
6 | 4 | inherited, monozygous triplet |
| Evaluated at 16 ys
| [17] |
7 | 4 | inherited, monozygous triplet |
| Evaluated at 16 ys
| [17] |
8 | 4 | inherited, daughter |
| Evaluated at 3.5 ys
| [17] |
9 | 5 | de novo |
| Evaluated at 5 ys
| [19] |
10 | 6 | de novo |
| Evaluated at 5 ys
| [19] |
11 | 7 | de novo |
| Evaluated at 4 ys
| [19] |
12 | 8 | de novo |
| Evaluated at 21 ys
| [19] |
13 | 9 | de novo |
| Evaluated at 32 ys
| [19] |
14 | 10 | inherited, daughter |
| Evaluated at 45 ys
| [19] |
15 | 10 | inherited, daughter |
| Evaluated at 45 ys
| [19] |
16 | 10 | inherited, niece |
| Evaluated at 17 ys
| [19] |
17 | 10 | inherited, niece |
| Evaluated at 6 ys
| [19] |
18 | 11 | not known, mother |
| Evaluated at 55 ys
| [19] |
19 | 11 | inherited, daughter |
| Evaluated at 24 ys
| [19] |
20 | 12 | not known, mother |
| Evaluated at 54 ys
| [19] |
21 | 13 | not known, daughter |
| Evaluated at 36 ys
| [19] |
22 | 14 | not known, mother |
|
| [19] |
23 | 14 | inherited, daughter |
| Evaluated at 7 ys
| [19] |
Case | Fam No. | Familiar/ De Novo | Mutation Type | Degree of Intellectual Disability (ID) | Reference |
---|---|---|---|---|---|
1 | 1 | de novo | -Glu1283* c.3847 G>T | MODERATE | Our case |
2 | 2 | de novo | -Met506Val c.1516 A>G | NO ID | [20] |
3 | 3 | inherited | -Val583Phe c.1747 G>T | NO ID | [4] |
4–8 | 4 | familiar | -Met1_Glu165del c.2T>C | Variable: MILD (in two patients), MODERATE, NO ID, DEVELOPMENTAL DELAY | [17] |
9 | 5 | de novo | -Ala50Argfs*23 c.147del | MODERATE | [19] |
10 | 6 | de novo | -Leu197Profs*23 c.589dup | MODERATE | [19] |
11 | 7 | de novo | -c.1243-2A>G -splicing | MODERATE | [19] |
12 | 8 | de novo | -Trp622Cys c.1866G>T | MODERATE | [19] |
13 | 9 | de novo | -Arg795Glyfs*5 c.2383_2384del | MODERATE | [19] |
14–17 | 10 | familiar | -Asp87Gly c.260A>G | Variable: MILD (3 patients), MODERATE | [19] |
18–19 | 11 | not known | -Trp52Cys c.156 G>T | Variable: MILD, MODERATE | [19] |
20 | 12 | not known | -Arg599Cys c.1795 C>T | NO ID | [19] |
21 | 13 | not known | -Glu613Lys c.1837 G>A | MILD | [19] |
22–23 | 14 | familiar | -c.2622 +2 dup | Variable: MILD, MODERATE | [19] |
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Lintas, C.; Bottillo, I.; Sacco, R.; Azzarà, A.; Cassano, I.; Ciccone, M.P.; Grammatico, P.; Gurrieri, F. Expanding the Spectrum of KDM5C Neurodevelopmental Disorder: A Novel De Novo Stop Variant in a Young Woman and Emerging Genotype–Phenotype Correlations. Genes 2022, 13, 2266. https://doi.org/10.3390/genes13122266
Lintas C, Bottillo I, Sacco R, Azzarà A, Cassano I, Ciccone MP, Grammatico P, Gurrieri F. Expanding the Spectrum of KDM5C Neurodevelopmental Disorder: A Novel De Novo Stop Variant in a Young Woman and Emerging Genotype–Phenotype Correlations. Genes. 2022; 13(12):2266. https://doi.org/10.3390/genes13122266
Chicago/Turabian StyleLintas, Carla, Irene Bottillo, Roberto Sacco, Alessia Azzarà, Ilaria Cassano, Maria Pia Ciccone, Paola Grammatico, and Fiorella Gurrieri. 2022. "Expanding the Spectrum of KDM5C Neurodevelopmental Disorder: A Novel De Novo Stop Variant in a Young Woman and Emerging Genotype–Phenotype Correlations" Genes 13, no. 12: 2266. https://doi.org/10.3390/genes13122266
APA StyleLintas, C., Bottillo, I., Sacco, R., Azzarà, A., Cassano, I., Ciccone, M. P., Grammatico, P., & Gurrieri, F. (2022). Expanding the Spectrum of KDM5C Neurodevelopmental Disorder: A Novel De Novo Stop Variant in a Young Woman and Emerging Genotype–Phenotype Correlations. Genes, 13(12), 2266. https://doi.org/10.3390/genes13122266