Compound heterozygosity for loss-of-function FARSB variants in a patient with classic features of recessive aminoacyl-tRNA synthetase-related disease

Abstract

Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes that ligate amino acids onto tRNA molecules. Genes encoding ARSs have been implicated in phenotypically diverse dominant and recessive human diseases. The charging of tRNA^PHE with phenylalanine is performed by a tetrameric enzyme that contains two alpha (FARSA) and two beta (FARSB) subunits. To date, mutations in the genes encoding these subunits (FARSA and FARSB) have not been implicated in any human disease. Here, we describe a patient with a severe, lethal, multisystem, developmental phenotype who was compound heterozygous for FARSB variants: p.Thr256Met and p.His496Lysfs*14. Expression studies using fibroblasts isolated from the proband revealed a severe depletion of both FARSB and FARSA protein levels. These data indicate that the FARSB variants destabilize total phenylalanyl-tRNA synthetase levels, thus causing a loss-of-function effect. Importantly, our patient shows strong phenotypic overlap with patients that have recessive diseases associated with other ARS loci; these observations strongly support the pathogenicity of the identified FARSB variants and are consistent with the essential function of phenylalanyl-tRNA synthetase in human cells. In sum, our clinical, genetic, and functional analyses revealed the first FARSB variants associated with a human disease phenotype and expand the locus heterogeneity of ARS-related human disease.

Keywords: FARSB; aminoacyl-tRNA synthetase; developmental syndrome; loss-of-function mutations; phenylalanyl-tRNA synthetase; recessive disease.

Figure 1

Head MRI, liver pathology, and chest CT of the proband. A and B: Coronal and sagittal T1-weighted head MRI images obtained at 5 months corrected age showing incomplete closure of the Sylvian fissures (asterisk in A), and bilateral frontoparietal cerebral volume loss (asterisk in B). C–F: Liver pathology. Architectural distortion (4X) with nodular formation (C); portal chronic inflammation with focal steatosis (10X) (D); Masson trichrome stain (2X) with well-developed cirrhosis and bridging fibrosis (E); and CK7 immunostain (4X) showing extensive bile ductular reaction (F). G and H: Chest CT (18 months) showing subpleural cystic changes (arrows) and interstitial disease.

Figure 2

Characterization of the FARSB variants identified in the proband. A: A simplex pedigree is shown with squares representing males and circles representing females. Genotypes are indicated under each symbol for the father, mother, and male proband (filled square). The proband is the only affected individual in the pedigree. B: The position of the p.Thr256Met variant is shown along with surrounding amino acid sequences for multiple, evolutionarily diverse species. Species are indicated along the left and the position of the affected residue is indicated by an arrow and bold text. C: Western blot analyses were performed using total protein lysates from fibroblasts isolated from two control individuals and from the patient described in this study, the latter performed in duplicate (Sample 1 and Sample 2). An anti-FARSB or anti-eIF2α antibody was employed to test for the effect of the FARSB variants on protein levels and to control for protein loading, respectively. Sample names are provided across the top of the panel and sizes in kDa are indicated on the right. D: Similar western blot analyses as described in panel C using an anti-FARSA antibody. In panels C and D, the ratio of FARSB or FARSA to eIF2α was determined by dividing the optical density of each FARS-specific band by that of the corresponding eIF2α-specific band.