Diagnosis of a patient with severe sensorineural hearing loss as the initial symptom caused by novel compound heterozygous variant in SLC19A2 gene

Abstract

Objective: Thiamine-Responsive Megaloblastic Anemia (TRMA) syndrome, caused by biallelic variants in the SLC19A2 gene, typically presents with a triad of megaloblastic anemia, diabetes mellitus, and sensorineural hearing loss. This study aims to determine the genetic etiology and clinical phenotype of a patient who presented with severe sensorineural hearing loss as the initial symptom, and to expand our understanding of the SLC19A2 variant spectrum.

Methods: Proband-only whole-exome sequencing was performed to screen the candidate variants, which were subsequently validated by Sanger sequencing within the family. cDNA sequencing based on RT-PCR and TA cloning analysis was used to determine the effect of splicing variants on mRNA processing of SLC19A2 gene. Detailed clinical features were evaluated by a diagnostic hearing test, laboratory and imaging examination.

Results: A 2-year-5-month-old Chinese girl was diagnosed with diabetes mellitus and severe sensorineural hearing loss, without abnormal hemoglobin. DNA sequencing revealed a novel compound heterozygous variant of c.808-1G > A and c.1228C > T (p.Gln410*) in the SLC19A2 gene. Both variants were previously unreported. The c.808-1G > A splicing variant is located in intron 2 of SLC19A2, and is predicted to cause exon 3 skipping. The cDNA experiment confirmed this biological event, further indicating that the splicing variant can cause amino acid frameshift alteration (p.Glu270Valfs*10) in SLC19A2.

Conclusion: We report a patient with TRMA syndrome (without anemia) caused by a novel compound heterozygous variant in SLC19A2 gene. This study suggests that the possibility of TRMA syndrome should be considered when encountering patients with early-onset severe sensorineural hearing loss in clinical practice.

Level of evidence: Level 4.

Keywords: Functional study; Novel compound heterozygous variant; SLC19A2 gene; Sensorineural hearing loss; Thiamine-responsive megaloblastic anemia syndrome.

Fig. 1

The results of hearing examination of the patient. (A) Pedigree of the family. Males are indicated by squares and females are indicated by circles. Generations are labeled using Roman numerals (I, II). Solid symbols indicate affected individuals. Arrow indicates the proband. (B) Upon conducting the Otoacoustic Emissions (OAE) test, no responses were elicited at any frequency in either ear. (C) Air conduction Auditory Brainstem Response (ABR) showed the threshold in both ears was 95 dB nHL. (D) No response in both ears at 40 dB nHL intensity upon bone conduction ABR test. (E) Auditory Steady-State Response (ASSR) test showed no response in the right ear at sound intensities above 95 dB nHL, whereas the left ear exhibited a response even under high-intensity stimulation. Red and blue indicate thresholds for the right and left ears, respectively.

Fig. 2

Genetic sequencing results of the family. Sanger sequencing confirmed the patient harbored the compound heterozygous variant of c.808-1G > A and c.1228C > T (p.Gln410*) in the SLC19A2 gene (NM_006996.3), which were inherited from the mother and father, respectively. Red arrows indicate the variant base.

Fig. 3

Splicing assays of the c.808-1G > A variant. (A) Schematic representation to show the location of the primers and the expected size of the PCR fragment in Wild-Type (WT) sample. (B) Electrophoresis was used to analyze the RT‑PCR results. A novel smaller band was observed in the patient and her mother’s samples. (C) Direct sequencing confirmed that the expected 463-bp band results from normal splicing of exons 2–4 in the SLC19A2 gene. (D) Clone sequencing revealed that the formation of the novel smaller band due to exon 3 skipping of SLC19A2.