A homozygous single-nucleotide variant in TNNT1 causes abnormal troponin T isoform expression in a patient with severe nemaline myopathy: A case report.

Background: Slow skeletal troponin T (ssTnT, TNNT1) is the tropomyosin-binding subunit of the troponin complex in the slow-twitch fibers of skeletal muscle. Exon 5 of TNNT1 is alternatively spliced, and retention of the 3' region of intron 11 (exon 12') has also been described. Variants in TNNT1 are known to cause nemaline myopathy (NM).

Objective: To identify and further investigate the disease-causing variant in a patient with lethal NM.

Methods: The genetic analyses included a gene panel, Sanger sequencing, whole-exome sequencing, and targeted array-CGH. Muscle biopsy was analyzed using routine histopathological methods. The alternative splicing of TNNT1 exon 12 in patient muscle was quantified from RNA sequencing data, and the protein expression was confirmed by western blot. Expression of ssTnT in patient muscle was studied by immunohistology.

Results: The patient presented with arthrogryposis, stiffness, respiratory insufficiency, and minimal spontaneous movements. Histopathology showed hypotrophy and predominance of type II fibers, perimysial connective tissue accumulation, and nemaline bodies. The patient was homozygous for the TNNT1 missense variant (NM_003283.6:c.653C > G, p.(Pro218Arg), NM_ 001126132.3:c.612-7C > G), predicted to disrupt splicing. RNA-seq revealed inclusion of exon 12' in 49.85% of transcripts, whereas in controls exon 12' was not expressed. Exon 12' expression on the protein level was confirmed by western blot. Immunohistology showed strong ssTnT expression in remaining type I fibers, and low expression in type IIA fibers.

Conclusions: The c.653C > G variant was shown to alter TNNT1 splicing. The results suggest a novel pathogenetic mechanism involving abnormal expression of a troponin T isoform.