The congenital myopathies are a genetically heterogeneous group of skeletal muscle disorders characterized by early onset muscle weakness and variable myopathic findings on muscle biopsy of which a third of patients remain genetically uncharacterized. Biallelic variants in NEB, encoding nebulin, are a known cause for nemaline myopathy; however, given NEB’s 183 exon expanse, and complexity of resulting isoforms, the functional impact of variants can be difficult to interpret. RNA sequencing is an emerging tool for understanding how such variants impact transcription and cause disease. Recently it has been shown that NEB contains alternatively spliced exons 143 and 144 (E144) and a role for specific isoforms in myogenesis and fiber typing has been postulated, with E144 showing predominant inclusion in the adult isoform of nebulin.
We present two brothers (11 and 15 years) with congenital myopathy with myopathic muscle biopsy findings without nemaline rods, normal CK, myopathic findings on EMG, and normal cardiac and pulmonary function. Quartet exome sequencing identified compound heterozygous variants in NEB (NM_001271208.2), a maternally inherited p.Cys693Ter and a paternally inherited c.21522+3A>G splice variant with unknown impact as it is adjacent to alternatively spliced E144.
To evaluate this variant, we pursued RNA sequencing on muscle tissue. Patient’s transcriptome showed skipping of E144, in contrast to controls who express a transcript ratio of approximately 1:3 (143:144) suggesting that the disease may partially be driven by a lack of NEB E144 inclusion, thus affecting the predominant adult isoform. Given this evidence, we compared patterns of muscle involvement from ultrasound and MRI to the literature to assess if the pattern of muscle involvement in our patient correlated to relative expression of E144 in adult muscle.
This case highlights the usefulness of RNA sequencing in evaluating genetic variants and for providing insight into the potential role of isoforms in disease pathogenesis.