Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish


Aminoacyl tRNA synthetases (ARSs) link specific amino acids with their cognate transfer RNAs in a critical early step of protein translation. Mutations in ARSs have emerged as a cause of recessive, often complex neurological disease traits. Here we report an allelic series consisting of seven novel and two previously reported biallelic variants in valyl-tRNA synthetase (VARS) in ten patients with a developmental encephalopathy with microcephaly, often associated with early-onset epilepsy. In silico, in vitro, and yeast complementation assays demonstrate that the underlying pathomechanism of these mutations is most likely a loss of protein function. Zebrafish modeling accurately recapitulated some of the key neurological disease traits. These results provide both genetic and biological insights into neurodevelopmental disease and pave the way for further in-depth research on ARS related recessive disorders and precision therapies.


Aminoacyl tRNA synthetases (ARSs) play a key role in protein translation as they catalyze the attachment of specific amino acids to their cognate transfer RNA (tRNA) molecules1,2. The nuclear encoded ARS gene loci are subdivided into 17 cytoplasmic, 17 mitochondrial, and three bi-functional ARSs3,4. The canonical aminoacylation and proofreading functions of ARSs are highly conserved across species. In addition, during evolution many ARSs acquired additional domains with unique structural characteristics that are not essential for tRNA charging but account for non-canonical functions5,6. These alternative functions are critical for cellular homeostasis and include among others: regulation of signal transduction and cell migration, angiogenesis and tumorigenesis, inflammatory responses, and control of cell death5. This functional diversity may in part account for the association between mutations in ARS genes and a broad range of human disorders, including neurological disorders, cancer, and auto-immune diseases2.

Both monoallelic and biallelic pathogenic variants in ARS genes, encoding dominant and recessive disease traits, respectively, have been increasingly reported in patients with various disorders that often have predominantly neurological features. Dominant heterozygous mutations in ARS genes have been identified in patients with Charcot-Marie-Tooth disease and related peripheral neuropathies, including AARS7, GARS8, HARS9,10, MARS11,12, WARS13, and YARS12,14. Recessive mutations have been identified in complex disorders often involving the central nervous system such as hypomyelination with brainstem and spinal cord involvement (DARS)15, leukodystrophy (RARS)16, congenital visual impairment and progressive microcephaly (KARS)17, developmental delay with progressive microcephaly and intractable seizures (QARS)18,19 and early onset epileptic encephalopathy with myelination defect (AARS)20. Interestingly, some ARS genes have been associated with both dominant and recessive disease traits including mutations in AARS7,20KARS21, and YARS14,22.

In this study, we report five newly diagnosed families with biallelic variants in valyl-tRNA synthetase (VARS), including seven novel VARS variants. In addition, we present an in-depth description of two families previously reported in a large study on brain malformations in mainly consanguineous families wherein VARS was reported as a candidate disease gene23. In vitro studies with patient-derived cell lines, including enzymatic assays, and yeast complementation assays show that recessive VARS mutations most likely lead to a loss-of-protein function, i.e. loss of function (LoF) alleles. A vars knockout (KO) zebrafish model further demonstrates that deficiency of vars results in microcephaly and epileptiform activity, replicating key characteristics of the human disease.


Biallelic VARS variants cause developmental encephalopathy

In total, ten patients from seven families with biallelic VARS variants were identified (Fig. 1a)23. All families were included through international collaborations or via the program GeneMatcher24. All patients had global developmental delay (DD), which was already present in the first months of life in most patients, and prior to seizure onset or unrelated to epilepsy in five patients. All patients at a sufficient age for IQ testing had severe or profound intellectual disability (ID) and were nonverbal. Only two of the nine patients who had reached the walking age were able to walk independently, though both acquired this skill only at later age.


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