Abstract
We ascertained two unrelated consanguineous families with two affected children each having microcephaly, refractory seizures, intellectual disability, and spastic quadriparesis. Magnetic resonance imaging showed atrophy of cerebrum, cerebellum and spinal cord, prominent cisterna magna, symmetric T2 hypo-intensities in the bilateral basal ganglia and thinning of corpus callosum. Whole-exome sequencing of three affected individuals revealed c.105C>A [p.(Tyr35Ter)] variant in AIMP2. The variant lies in a common homozygous region of 940 kb on chromosome 7 and is likely to have been inherited from a common ancestor. The phenotype noted in our subjects’ shares marked similarity with that of hypomyelinating leukodystrophy-3 caused by mutations in closely related gene AIMP1. We hereby report the first human disease associated with deleterious mutations in AIMP2.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Robinson JC, Kerjan P, Mirande M. Macromolecular assemblage of aminoacyl-tRNA synthetases: quantitative analysis of protein-protein interactions and mechanism of complex assembly. J Mol Biol. 2000;304:983–94.
Kim JH, Han JM, Kim S. Protein-protein interactions and multi-component complexes of aminoacyl-tRNA synthetases. Top Curr Chem. 2014;344:119–44.
Ognjenovic J, Simonovic M. Human aminoacyl-tRNA synthetases in diseases of the nervous system. RNA Biol. 2017. https://doi.org/10.1080/15476286.2017.1330245.
Guo Y, Ding X, Shen Y, Lyon GJ, Wang K. SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Sci Rep. 2015;5:14283. https://doi.org/10.1038/srep14283.
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164. https://doi.org/10.1093/nar/gkq603.
Girisha KM, Shukla A, Trujillano D, Bhavani GS, Hebbar M, Kadavigere R, et al A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Clin Genet. 2016;90:536–9.
Vigeland MD, Gjotterud KS, Selmer KK. FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector. Bioinformatics. 2016;32:1592–4.
Shukla A, Hebbar M, Srivastava A, Kadavigere R, Upadhyai P, Kanthi A, et al Homozygous p.(Glu87Lys) variant in ISCA1 is associated with a multiple mitochondrial dysfunctions syndrome. J Hum Genet. 2017. https://doi.org/10.1038/jhg.2017.35.
Aggarwal S, Das Bhowmik A, Ramprasad VL, Murugan S, Dalal A. A splice site mutation in HERC1 leads to syndromic intellectual disability with macrocephaly and facial dysmorphism: further delineation of the phenotypic spectrum. Am J Med Genet. 2016;170A:1868–73.
Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310–5.
Schimmel PR, Soll D. Aminoacyl-tRNA synthetases: general features and recognition of transfer RNAs. Annu Rev Biochem. 1979;48:601–48.
Yao P, Fox PL. Aminoacyl-tRNA synthetases in medicine and disease. EMBO Mol Med. 2013;5:332–43.
van der Knaap MS, van der Voorn P, Barkhof F, Van, Coster R, Krägeloh-Mann I, Feigenbaum A, et al A new leukoencephalopathy with brainstem and spinal cord involvement and high lactate. Ann Neurol. 2003;53:252–8.
Feinstein M, Markus B, Noyman I, Shalev H, Flusser H, Shelef I, et al Pelizaeus-Merzbacher-like disease caused by AIMP1/p43 homozygous mutation. Am J Hum Genet. 2010;87:820–8.
Quevillon S, Robinson JC, Berthonneau E, Siatecka M, Mirande M. Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein. J Mol Biol. 1999;285:183–95.
Park SG, Choi EC, Kim S. Aminoacyl-tRNA synthetase-interacting multifunctional proteins (AIMPs): a triad for cellular homeostasis. IUBMB Life. 2010;62:296–302.
Cestari I, Kalidas S, Monnerat S, Anupama A, Phillips MA, Stuart K. A multiple aminoacyl-tRNA synthetase complex that enhances tRNA-aminoacylation in African trypanosomes. Mol Cell Biol. 2013;33:4872–88.
Kim JY, Kang YS, Lee JW, Kim HJ, Ahn YH, Park H, et al. p38 is essential for the assembly and stability of macromolecular tRNA synthetase complex: implications for its physiological significance. Proc Natl Acad Sci USA. 2002;99:7912–6.
Sobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat. 2015;36:928–30.
Acknowledgements
We thank the families who cooperated with the evaluation of the subjects and consented for participation in this study. We are also thankful to Dr. Vineeth VS & Dr. Usha R Dutta from Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad for assisting in RT-qPCR experiment. Our sincere thanks to Ms. Priyanka Bhakt and Dr. Rupinder Kaur from the Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad for assisting in statistical analysis of RT-qPCR using GraphPad Prism software.
Funding
This work was supported by the Department of Health Research, which funded the project titled “Clinical and molecular characterization of leukodystrophies in Indian children” (V.25011/379/2015-GIA/HR) and Science and Engineering Research Board (SERB), Government of India (SERB file no. YSS/2015/001681) and Department of Biotechnology, Government of India, Grant Number: BT/PR3193/MED/12/521/2011.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Shukla, A., Das Bhowmik, A., Hebbar, M. et al. Homozygosity for a nonsense variant in AIMP2 is associated with a progressive neurodevelopmental disorder with microcephaly, seizures, and spastic quadriparesis. J Hum Genet 63, 19–25 (2018). https://doi.org/10.1038/s10038-017-0363-1
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s10038-017-0363-1
This article is cited by
-
Assessment the Efficacy of the CRISPR System for Inducing Mutations in the AIMP2 Gene to Create a Cell Line Model of HLD17 Disease
Molecular Biotechnology (2025)
-
Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m6A site accessibility
Nature Communications (2024)
-
Knockdown of Golgi Stress-Responsive Caspase-2 Ameliorates HLD17-Associated AIMP2 Mutant-Mediated Inhibition of Oligodendroglial Cell Morphological Differentiation
Neurochemical Research (2022)
-
Roles of aminoacyl-tRNA synthetase-interacting multi-functional proteins in physiology and cancer
Cell Death & Disease (2020)
-
Clinical Features of Patients With 7p22.1 Microdeletion
Indian Pediatrics (2020)