Nemaline Myopathy Panel

Nemaline myopathy (NM) is a genetically and clinically heterogeneous disorder characterized by muscle weakness, hypotonia and the presence of nemaline bodies in skeletal muscle fibers. Muscle weakness is typically observed in affected neonates or infants, although later onset cases are reported (Ryan et al. 2001). The most severely affected muscle groups are proximal limb, facial, bulbar, and respiratory muscles. Deep tendon reflexes are absent or depressed. Histologically, NM is characterized by type 1 fiber predominance and the presence of rod-like structures called nemaline bodies upon Gomori trichrome staining of skeletal muscle (Ryan et al. 2003). Six clinical types of NM have been delineated based on age of onset, severity and distribution of weakness, and respiratory function (Ryan et al. 2001; North and Ryan. 2015). Overlap among the six clinical groups is significant and adults are sometimes diagnosed only after another family member has presented with typical signs. Nebulin gene pathogenic variants most often cause typical neonatal onset disease, although NEB pathogenic variants have been found in every clinical form of NM (Lehtokari et al. 2006). Troponin T1 associated NM is a lethal disorder described only in the Old Order Amish community of Pennsylvania (Johnston et al. 2000). Nemaline myopathy-8 due to pathogenic variants in the KLHL40 gene represents a severe form of this disease with features of fetal akinesia or hyopkinesia and early lethality (Ravenscroft et al. 2013).

Pathogenic variants in a growing number of genes have been shown to cause nemaline myopathy. Most forms of nemaline myopathy (NEB, CFL2, KLHL40, KLHL41, LMOD3 and TNNT1) are inherited as autosomal recessive diseases, although ACTA1 or TPM3-related nemaline myopathy can be inherited as a dominant or recessive condition. TPM2 and KBTBD13-related nemaline myopathy are inherited as autosomal dominant conditions (Nowak et al 2015). Pathogenic variants in NEB and ACTA1 are the only relatively common causes accounting for up to 50% and 15-25%, respectively, of all studied cases (Ryan et al. 2001; North and Ryan 2015). The majority of reported NEB pathogenic variants (Lehtokari et al. 2014) are splice site variants (34%), frameshift (32%), and nonsense (23%). Reported pathogenic missense variants appear to be less common (~7%). The only common NEB pathogenic variant is an exon 55 deletion found at a carrier frequency of about 1% among people of Ashkenazi Jewish ancestry (Anderson et. al. 2004). ACTA1 missense variants are a major type of reported dominant pathogenic variants and are commonly associated with sporadic (de novo) cases. Recessive ACTA1-related myopathy is very rare, usually due to null ACTA1 pathogenic variants, in the compound heterozygous state with pathogenic missense variants (Laing et al. 2009; http://www.LOVD.nl/ACTA1). See individual gene test descriptions for information on molecular biology of gene products.

Nebulin gene pathogenic variants are most common cause of Nemaline Myopathy, accounting for up to 50% of cases (Ryan et al. 2001; North and Ryan 2002). ACTA1 pathogenic variants account for 15%-25% of all individuals with NM (Laing et al. 2009). Eight other genes (TPM3, TNNT1, TPM2, CFL2, LMOD3, KBTBD13, KLHL40, KLHL41) are involved with NM, however, the fraction of cases attributed to each of them is small. Deletion of exon 55 of NEB occurs with a carrier frequency of ~1% among people of Ashkenazi Jewish ancestry (Anderson et al. 2004).

Clinical sensitivity for deletion/duplication testing is expected to be low. One exception is the Ashkenazi Jewish nebulin exon 55 deletion.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 88.5% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Exons 82-105 of the NEB gene are organized in three highly homologous blocks of 8 exons each making this region difficult to analyze by NextGen Sequencing only and are not included in this test.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).