A Novel and Mosaic WDR45 Nonsense Variant Causes Beta-Propeller Protein-Associated Neurodegeneration Identified Through Whole Exome Sequencing and X chromosome Heterozygosity Analysis
Beta-propeller protein-associated neurodegeneration (BPAN) is an X-linked rare dominant disorder of autophagy. The role of WDR45 has been implicated in BPAN almost exclusively in females possibly due to male lethality. Characterization of distinctive clinical manifestations and potentially the complex genetic determinants in rare male patients remain crucial for deciphering BPAN and other X-linked dominant diseases. We performed whole exome sequencing (WES) followed by segregation analysis and identified a novel nonsense and mosaic variant in WDR45, namely NM_007075.3:c.873C>G; p.(Tyr291*) in an affected male at the age of 34. His biphasic medical history was compatible with BPAN, which was characterized by delayed psychomotor development, intellectual disability, and progression into dystonia parkinsonism in his twenties. The variant had an apparently mosaic pattern both in whole exome and Sanger sequencing findings. In order to figure out if mosaicism was restricted to this variant or related to a chromosomal level mosaicism, we used our in-house WES data from 129 unrelated individuals to calculate the threshold values of male and female X chromosome heterozygosity (XcHet) in WES data for our pipeline. A background level of heterozygous variants on X chromosome excluding the pseudoautosomal loci is an observed phenomenon in WES analysis and this level has been used as a quality measure. Herein, we suggest utilization of this measure for detection of digital anomalies of the X chromosome in males by potentially observing a higher XcHet value than the threshold value. This approach has revealed a variant level mosaicism in the affected male, which was further supported with cytogenetic analyses.
KeywordsWDR45 Mosaicism Whole exome sequencing X chromosome heterozygosity BPAN
The authors wish to thank the patient and his family for participating in this study. This work was supported by grant from the Scientific Research Projects Coordination Unit of Istanbul University, Project Number TDK-2017-26646.
This study was funded by the Scientific Research Projects Coordination Unit of Istanbul University, Project Number TDK-2017-26646.
Compliance with Ethical Standards
Conflict of interest
The authors declare that they have no conflict of interest.
This study was approved by the Ethics Committee of Istanbul Faculty of Medicine, Istanbul University (protocol number 2017/113). Written consent was received from patients family authorizing us to use his medical data in this publication.
Informed consent was obtained from all individual participants included in the study. Additional informed consent was obtained from all individual participants for whom identifying information is included in this article.
- Civelli, O., & Zhou, Q. (2007). Dopamine receptors: Molecular pharmacology. Encyclopedia of life sciences. Hoboken: Wiley.Google Scholar
- Coban-Akdemir, Z., White, J. J., Song, X., Jhangiani, S. N., Fatih, J. M., Gambin, T., Bayram, Y., Chinn, I. K., Karaca, E., Punetha, J., et al. (2018). Identifying genes whose mutant transcripts cause dominant disease traits by potential gain-of-function alleles. American Journal of Human Genetics, 103, 1–17.CrossRefGoogle Scholar
- Haack, T. B., Hogarth, P., Kruer, M. C., Gregory, A., Wieland, T., Schwarzmayr, T., Graf, E., Sanford, L., Meyer, E., Kara, E., et al. (2012). Exome sequencing reveals de novo WDR45 mutations causing a phenotypically distinct, X-linked dominant form of NBIA. American Journal of Human Genetics, 91, 1144.CrossRefPubMedPubMedCentralGoogle Scholar
- Kruer, M. C., Boddaert, N., Schneider, S. A., Houlden, H., Bhatia, K. P., Gregory, A., Anderson, J. C., Rooney, W. D., Hogarth, P., & Hayflick, S. J. (2012). Neuroimaging features of neurodegeneration with brain iron accumulation. American Journal of Neuroradiology. 33, 407iol.c.CrossRefGoogle Scholar
- McKinney, W. (2011). pandas: A Foundational Python Library for Data Analysis and Statistics, PyHPC2011.Google Scholar
- Redon, S., Benech, C., Schutz, S., Despres, A., Gueguen, P., Le Berre, P., Le Marechal, C., Peudenier, S., Meriot, P., Parent, P., et al. (2017). Intragenic deletion of the WDR45 gene in a male with encephalopathy, severe psychomotor disability, and epilepsy. American Journal of Medical Genetics Part A, 9999, 1–3.Google Scholar
- Takano, K., Goto, K., Motobayashi, M., Wakui, K., Kawamura, R., Yamaguchi, T., Fukushima, Y., & Kosho, T. (2017). Early manifestations of epileptic encephalopathy, brain atrophy, and elevation of serum neuron specific enolase in a boy with beta-propeller protein-associated neurodegeneration. European Journal of Medical Genetics, 60(10), 521–526.CrossRefPubMedGoogle Scholar
- Taudien, S., Lausser, L., Giamarellos-Bourboulis, E.J., Sponholz C., Schöneweck, F., Felder, M., Schirra, L.R., Schmid F., Gogos C., Groth, S. et al. (2016). Genetic factors of the disease course after sepsis: Rare deleterious variants are predictive. EBioMedicine 12, 227–238.CrossRefPubMedPubMedCentralGoogle Scholar
- Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., et al. (2013). From FastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics., 43, 11.PubMedGoogle Scholar
- BrainSpan, Retrieved from http://www.brainspan.org/.
- Variant Effect Predictor-Ensembl. Retrieved from https://www.ensembl.org/info/docs/tools/vep/index.html/.