Clinical information
Proband A and Pedigree A
The patient was a 6 years and 3 months old boy, who was born in a non-consanguineous family. He was the first child of a mother with histories of obstetric complications including one induced abortion due to side effects of antifungal medication and a spontaneous abortion of unknown cause. In addition, the mother had an early threatened miscarriage during the pregnancy of probands A, but she got a remission after immediate medical intervention. The case was delivered at full-term via caesarian section. The physical examination was unremarkable at birth.
The first noticeable clinical characteristic of this case was a profound global developmental delay which was noted since his infancy. His gross and fine motor skills were acquired and improved slowly: neck muscle control was achieved at the age of 15 months, sit with support at the age of 4 years, walk dependently, and inflexible finger movements at the last follow up (6 years and 3 months). Besides, he had a cognitive impairment and difficulties in language acquisition. At the last follow up, he only could understand some simple terms such as his nickname or some simple instructions, but could not speak a word. There has been no aggressive behavior noticed in proband A so far. Moreover, his daily life needed to be fully taken care of by others. Complex febrile seizures were observed in the course: one episode occured at the age of 1 year and the second one at the age of 2 years. he electroencephalogram (EEG) and magnetic resonance imaging (MRI) of the brain done at 4 years old age were normal. Meanwhile, the development quotients for adaptability, gross motor movements, fine motor movements, language, and individual–social interaction on the Gesell developmental scales were 36, 41, 30, 43, and 50, respectively. Other laboratory examinations including the routine blood biochemical tests, metabolic analyses yielded negative. He had a medical history of bilateral esotropia.
This case had a healthy younger brother whose age was two years old at the last follow up (Fig. 1a). His mother had no neurological signs. Noticeably, epileptic seizures were also observed in his biological father's childhood, which began with febrile seizures, then evolved to afebrile attacks. But his symptoms disappeared in adulthood. There was no other family history of neurological disorders to disclose.
Proband B and Pedigree B
An 8.5-year-old boy presenting with intellectual disability, epilepsy, abnormal social behavior, and ametropia came to our center's clinic. The patient was born as a third child of non-consanguineous healthy parents after uneventful pregnancy and delivery. A distant uncle of the proband was diagnosed with intellectual disability, and his older female cousin was noticed to have a mood disorder.
The first remarkable seizure was observed when aged 7 years. The manifestations of the seizures included the sudden loss of consciousness, rigidity of the limbs, and lips cyanosis, which lasted for minutes. Besides, he had post-ictal fatigue, and experienced 1-3 seizure episodes per year. His EEG revealed occasional sharp-waves were observed in bilateral frontal areas during sleep, but absent during the wake time. Brain MRI did not reveal significant structural abnormalities. His seizure was easily controlled by taking Levetiracetam, but he still lagged behind his peers in intelligence development (he had poor performance in school and could not communicate well with others). His intelligence quotient score at 8.5-year-old was 50.9. He also exhibited bad tempers, social problems, attention deficit, and hyperactivity. Nevertheless, the behavior assessments, including Conners' Comprehensive Behavior Rating Scales (CBRS), Kiddie-SADS DSM-5 Screen Interview (K-SADS-PL), and Autism Behavior Checklist (ABC) were negative. In addition, the proband was diagnosed with ametropia. Metabolic etiology, immunological etiology, and infectious etiology were excluded after the diagnostic workup.
The proband had two healthy elder sisters, 18 and 14 years old, respectively. They both performed well in school (Fig. 1b). His parents had low levels of education but worked, and thus they can support their family well.
Genetic findings
The karyotype and copy number variation results in probands A and B showed no abnormalities in their chromosomes. Maternal inherited SYN1 mutations were identified in both probands through the WES.
In the pedigree A, a missense variant in SYN1 exon 9: c.C1076A , p.T359K (NM_133499) was present in a hemizygous state in proband A and a heterozygous state in his mother, grandmother, and great-grandmother as an obligate carrier, but it was absent in his younger brother, father, and grandfather (Fig. 1a & Fig. 1c). The variant T359K has been reported as a variant of uncertain significance in ClinVar database records (accession VCV000589101.2), associated with a "history of neurodevelopmental disorder" [5]. However, no more detail clinical information of the patient was described in the database. The substitution of lysine for threonine acid at position 359 within domain C of SYN1 protein is considered "possibly damaging" (score 0.886) with PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/), "deleterious" (score -2.565) with PROVEAN (http://provean.jcvi.org/) and "disease-causing" (score 78) with MutationTaster (http://www.mutationtaster.org/).
In the pedigree B, a truncation variant in SYN1 exon 12: c.C1444T, p.Q482X (NM_133499) was identified, which was also present in a hemizygous state in proband B, and a heterozygous state in his mother but it was absent in his father (Fig. 1d). The variant validation of other family members was not done for financial reasons (Fig. 1b). The variant has never been reported before and cannot be found in dbSNP143, the 1000 Genomes Project database, and the Clinvar database. The nonsense mutation Q482X lies in the domain D of the protein and is identified as "disease-causing" (score 6) with MutationTaster (http://www.mutationtaster.org/).
Bioinformatic analysis showed that sites T359 and Q482 are highly conserved residues among different species (Fig. 1e). Both variants were classified as "Pathogenic," according to the ACMG guidelines4.