Expanding the phenotype of biallelic loss-of-function variants in the NSUN2 gene: Description of four individuals with juvenile cataract, chronic nephritis, or brain anomaly as novel complications
Funding information: Japan Agency for Medical Research and Development, Grant/Award Number: JP17ek0109281; JSPS
Abstract
The NSUN2 gene encodes a tRNA cytosine methyltransferase that functions in the maturation of leucyl tRNA (Leu) (CAA) precursors, which is crucial for the anticodon-codon pairing and correct translation of mRNA. Biallelic loss of function variants in NSUN2 are known to cause moderate to severe intellectual disability. Microcephaly, postnatal growth retardation, and dysmorphic facial features are common complications in this genetic disorder, and delayed puberty is occasionally observed. Here, we report four individuals, two sets of siblings, with biallelic loss-of-function variants in the NSUN2 gene. The first set of siblings have compound heterozygous frameshift variants: c.546_547insCT, p.Met183Leufs*13; c.1583del, p.Pro528Hisfs*19, and the other siblings carry a homozygous frameshift variant: c.1269dup, p.Val424Cysfs*14. In addition to previously reported clinical features, the first set of siblings showed novel complications of juvenile cataract and chronic nephritis. The other siblings showed hypomyelination and simplified gyral pattern in neuroimaging. NSUN2-related intellectual disability is a very rare condition, and less than 20 cases have been reported previously. Juvenile cataract, chronic nephritis, and brain anomaly shown in the present patients have not been previously described. Our report suggests clinical diversity of NSUN2-related intellectual disability.
1 INTRODUCTION
Biallelic loss-of-function variants in NSUN2 are responsible for moderate to severe intellectual disability (ID, MIM#611091) (Abbasi-Moheb et al., 2012; Khan et al., 2012). Affected patients were reported to have microcephaly, short stature, and some dysmorphic features, including long face, long nose, high nasal bridge, and smooth philtrum. Beside these phenotypes, other physical complications were not reported in most cases, although delayed puberty was described in some patients. Here, we report four patients, two sets of siblings, with biallelic loss-of-function variants in the NSUN2 gene. All four cases presented severe ID, short stature, and microcephaly. In addition, they also presented with previously undescribed complications of juvenile cataract, chronic nephritis, and brain anomaly. This information will expand the spectrum of the clinical diversity of patients with NSUN2 biallelic pathogenic variants.
2 CASE REPORT AND GENETIC TESTING
2.1 Patient 1
Patient 1 was female, born at 37 weeks gestation. She was the second child of unrelated and healthy Japanese parents. Pregnancy and delivery were uneventful, and her body size at birth including weight, length, and head circumference was normal. She was 16 years old at the most recent examination, and she had severe postnatal growth retardation with short stature (−6.0 SD) and microcephaly (−5.6 SD). She had some dysmorphic features including long face, smooth philtrum, full and downturned upper lip, and macrodontia (Figure 1a). Her development was globally delayed with walking achieved at 72 months and absent speech. The overall developmental quotient (DQ) was 12 at 12 years of age, as evaluated by the Kyoto Scale of Psychological Development (KPSD). She presented with sustained microscopic hematuria and proteinuria, although renal function had not declined at 16 years old. She was diagnosed with bilateral cataracts at 11 years of her age. In addition, she had moderate hearing impairment. She underwent anterior pituitary hormone loading test and some imaging studies at 16 years old, as she has not had menarche yet. The result of luteinizing hormone-releasing hormone (LH-RH) loading test and brain magnetic resonance imaging (MRI) were normal, but ultrasonography showed decreased size of the uterus with normal size of her ovary, indicating the possibility of ovarian dysfunction. Also, she was diagnosed as having a growth hormone (GH) deficiency, the peak GH level detected by an arginine or L-DOPA stimulation test was 1.71 and 1.06 mg/dl, respectively.
2.2 Patient 2
Patient 2 was a younger brother of patient 1. He was born at 38 weeks gestation with normal weight, length, and head circumference. His development was globally delayed with sitting at 13 months and walking at 48 months of age and absent speech. The overall DQ was 17 at 10 years of age, as evaluated by KPSD. He was 11 years old at the most recent examination, when he had postnatal growth retardation with short stature (−3.8 SD) and microcephaly (−3.4 SD). He had dysmorphic facial features with long face, smooth philtrum, full and downturned upper lip, and macrodontia (Figure 1b). Brain MRI performed at 5 years did not reveal any abnormality. He had an operation for cryptorchism at 19 months of age. He also had moderate hearing impairment, microscopic hemato-proteinuria, and bilateral cataracts. He underwent hormone loading test and some imaging studies at 14 years old, because, as with the case of his sister, he has not developed secondary sexual characteristics yet. LH-RH loading test showed the decreased peak level of LH 0.54 (mIU/ml) and FSH 3.96 (mIU/ml). In addition, GH deficiency was diagnosed, as the peak GH level detected by an arginine or L-DOPA stimulation test was 2.61 and 1.59 mg/dl, respectively.
2.3 Patient 3
Patient 3 was female, the third child of Pakistani parents of a married cousin, born at 42 weeks gestation and was small for gestational age with birth weight 2,600 g (second centile) and head circumference 33.5 cm (ninth percentile). She had some feeding difficulties in the initial period but did not require hospitalization. At 3 months, she presented with pyelonephritis. Investigations showed vesicoureteral reflux and slightly echogenic kidneys with loss of corticomedullary differentiation. Her development was globally delayed with starting to sit at 2 years and walk at 4 years. She had absent speech. She had no history of regression or seizures. Brain MRI at 4 years showed hypomyelination, a dysplastic corpus callosum and a simplified gyral pattern of the frontal lobe (Figure 1c). She had dysmorphic facial features with synophrys, large and short nose, broad nasal tip, full lip, and occipital flattening. She also had long fingers, toes. She had a deep midline coccygeal dimple and bilateral dimples overlying the iliac crests. She was 17 years at the most recent examination, but she had no signs of puberty. She had short stature and marked postnatal microcephaly (−6 SD). She had an ataxic gait, severe learning difficulties, and eczema.
2.4 Patient 4
Patient 4 is the younger brother of patient 3, and his clinical features are very similar to those of patient 3. He was born at 38 weeks gestation with a low birth weight 2.09 kg, and head circumference of 32 cm (below the second percentile). His development was globally delayed. He was 12 years old at the most recent examination, and he had short stature and marked microcephaly (−4 to −5 SD). He had ataxia and mild spasticity, but was able to walk with a walker. He had no speech and severe cognitive impairment. He had dysmorphic facial features with coarse facies, synophrys, large and short nose, broad nasal tip, full lips, and occipital flattening. Brain MRI taken at 1 year showed delayed myelination, a mildly dysplastic corpus callous, and simple frontal gyral pattern. He also had eczema and an absent left testis.
2.4.1 Genetic testing
Exome sequencing was performed on the affected siblings and their parents. As a result, we identified compound heterozygous loss-of-function variants in the NSUN2 gene (NM_017755: c.546_547insCT, p.Met183Leufs*13; c.1583del, p.Pro528Hisfs*19) in first set of affected siblings, each was inherited from mother and father, respectively (Supporting Information, Figure S1a). The identified variants were confirmed by Sanger sequencing. Of 19 exons, these variants are located at exons 6 and 14, respectively. Therefore, these frameshift variants were considered to induce nonsense mediated decay (NMD), resulting in a marked decrease in the NSUN2 mRNA expression. In patients 3 and 4, we identified a homozygous frameshift variant: c.1269dup, p.Val424Cysfs*14, in exon12 (Figure S1b). Collectively, we inferred that the biallelic loss-of-function variants in NSUN2 were responsible for the phenotype of cases in this study.
3 DISCUSSION
Here, we report patients, with biallelic loss-of-function variants in NSUN2, who presented with novel features of juvenile cataract, chronic nephritis, delayed myelination, and simple frontal gyral pattern in addition to previously reported features. A review of clinical manifestations and pathogenic variants in patients with NSUN2 deficiency previously reported in the literature is presented in Table S1 and Figure S1c. Except for one missense variant, all the reported variants were composed of splice site, frameshift, or nonsense variants. NSUN2 gene alterations have been reported to be responsible for an autosomal recessive intellectual disability syndrome with microcephaly, short stature, and dysmorphic facial features. In addition, delayed puberty is observed in some cases. Juvenile cataract and chronic nephritis, in the first pair of siblings we describe, have not previously been reported in patients with NSUN2 pathogenic variants. Also, to the best of our knowledge, brain anomalies have not yet been reported previously. The decreased response of GH and LH-RH loading test observed in the first pair of siblings indicated the importance of endocrinological analysis in patients with NSUN2 deficiency.
Various eye phenotypes including cataract and abnormal lens morphology have been reported in Nsuns2 knockout mice (Adissu et al., 2014). Hence, juvenile cataract shown in the present cases may be due to the NSUN2 pathogenic variants. As for the renal dysfunction, it is also reported as one of the complications associated with another tRNA modification-related disorder, like Galloway–Mowat syndrome caused by WDR4 dysfunction (Braun et al., 2018). Given that NSUN2 is an essential enzyme to catalyze the methylation of the tRNA precursor, which is crucial for translation, and the NSUN2 mRNA is reported to be ubiquitously expressed, we postulate that NSUN2 deficiency can cause renal abnormalities (Abbasi-Moheb et al., 2012).
In summary, we identified biallelic frameshift variants in the NSUN2 gene, in four patients with severe ID, microcephaly, and short stature. In addition, two of the patients presented with juvenile cataract and chronic nephritis, and the other two with brain anomaly including delayed myelination and simplified gyri. Our report expands the phenotypic diversity of patients with biallelic loss-of-function variants in NSUN2.
ACKNOWLEDGMENTS
The authors thank the patient and his parents for participating in this study. The authors thank Takahiro Yonekawa for endocrinological assessment of patients. This study was partially supported by JSPS KAKENHI Grant Number JP17ek0109281 (TO). This work was supported by AMED under Grant Number Table (T.O.).
CONFLICT OF INTEREST
None.
AUTHOR CONTRIBUTIONS
T.O. was responsible for the concept and design of the study. K.K. and T.O. drafted the main manuscript. K.K., S.M., and J.M. contributed clinical data. M.T. and Y.H. analyzed and interpreted the sequence data. E.W. and A.L. revised the manuscript and made comments on the structure, details and grammar of the article.
ETHICS STATEMENT
This study was approved by the Ethical Committee for the Study of Human Gene Analysis at Nagoya University Graduate School of Medicine. The patient's parents gave written consent for the publication of the clinical information, including photographs.
Open Research
DATA AVAILABILITY STATEMENT
The data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.
