Identification of a novel ST3GAL5 variant in a Chinese boy with GM3 synthase deficiency and literature review of variants in the ST3GAL5 gene

Case presentation

The patient was born to nonconsanguineous Chinese parents without apparent abnormalities. Neonatal jaundice was observed at birth, and promptly treated with blue-light therapy. At 3 months old, the child experienced a high fever of 39 °C, followed by generalized rigidity, clenched fists, staring eyes, and cyanosis of the lips, lasting 1 min and resolving spontaneously. By 5 months old, the child displayed poor interactions, weighing 6 kg (< 3rd percentile), with a length of 62.7 cm (> 3rd percentile), and a head circumference of 37.5 cm (< 3rd percentile). The fontanel remained open, and muscle strength and tone were diminished. Laboratory tests indicated increased blood amino acid metabolism, hyperlactatemia, and poor urea cycle function. Urine organic acid analysis revealed non-ketotic dicarboxylic aciduria, hepatic damage, and insufficient energy production. Cranial MRI showed a slight widening of the extracerebral space in the bilateral frontotemporal region. Chest radiography and CT indicated pneumonia and gastroesophageal ultrasound suggested gastroesophageal reflux. Audio-visual evoked potentials were abnormal, with increased ABR response thresholds in both ears. EEG findings were abnormal. Cranial CT, liver ultrasound, gallbladder ultrasound, pancreas ultrasound, spleen ultrasound, kidney ultrasound, and electrocardiography showed no abnormalities. Treatment with oxcarbazepine had limited efficacy. The patient was diagnosed with developmental delay, microcephaly, epilepsy, hyperlactatemia, and non-ketotic dicarboxylic aciduria. At 6 months old, the child exhibited hair thinning, abdominal distension, and an umbilical hernia. At 22 months old, the child returned to the hospital with a height of 75 cm (< 3rd percentile), weight of 6 kg (< 3rd percentile), and head circumference of 41 cm (< 3rd percentile). The patient experienced sudden shouting during sleep, fatigue, poor visual and auditory tracking abilities, unsteady neck, inability to crawl, sit, stand, or walk without support, nonverbal communication, constipation, inability to grasp objects, express needs, or follow simple commands, and lagged peers in cognitive and comprehension skills. These symptoms were consistent with previously reported clinical manifestations of GM3SD.

At 6 months old, the patient started oral oxcarbazepine for epilepsy. The patient is now 4 years old, and the frequency of the patient’s epileptic seizures has decreased from a maximum of three times a day at the beginning to only one occurrence in the past 2 years. The patient continued to experience dystonia and constipation, but with good parental care, feeding difficulties improved significantly, and pneumonia frequency decreased.

Identification of compound heterozygous mutations in the ST3GAL5 gene

Trio WES analysis was conducted on the proband and his parents, revealing compound heterozygous variants in ST3GAL5 (c.1000delC, p.Arg334Glufs*15 and c.207-1G > T, p.Cys70Glufs*81). Sanger sequencing of the patients and their parents confirmed that the mother carried a heterozygous variant of c.1000delC, while the father carried a heterozygous variant of c.207-1G > T (Fig. 1). Both heterozygous mutations were classified as likely pathogenic according to the ACMG guidelines.

Impairment of ST3GAL5 expression by compound heterozygous mutations c.1000delC and c.207-1G > T

To further elucidate the deleterious effects of ST3GAL5 mutations on its expression, in vitro experiments were performed. Expression vectors containing wild-type ST3GAL5 and mutated ST3GAL5 were constructed and transiently transfected into HEK293T cells. mRNA levels of ST3GAL5 were analyzed, revealing decreased expression in cells transfected with the mutated plasmid compared to the wild-type. Western blotting indicated that the protein produced by Arg334Glufs*15 was truncated, consisting of 348 amino acids, and confirmed to be pathogenic [2]. Conversely, the wild-type sample exhibited a ~ 50-KD band consistent with the expected molecular size of the ST3GAL5 protein, comprising 418 amino acid residues.

WES results suggested that the c.207-1G > T variant disrupts the original splice site. Minigene splicing experiments were conducted to validate the aberrantly spliced transcripts caused by this mutation. The results indicated that the c.207-1G > T mutation affected the normal splicing of ST3GAL5, resulting in an expression of c.207_318del, p.Cys70Glufs*81 due to exon 3 skipping. Overall deletion of exon 3 led to a change in the subsequent reading frame, producing a truncated protein.

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