| Literature DB >> 31127036 |
Minttu Marttila1, Wathone Win1, Fouad Al-Ghamdi1,2, Hoda Z Abdel-Hamid3,4, David Lacomis5, Alan H Beggs1.
Abstract
Next-generation sequencing has led to transformative advances in our ability to diagnose rare diseases by simultaneously sequencing dozens, hundreds, or even entire genomes worth of genes to efficiently identify pathogenic mutations. These studies amount to multiple hypothesis testing on a massive scale and not infrequently lead to discovery of multiple genetic variants whose relative contributions to a patient's disease are unclear. Panel testing, in particular, can be problematic because each of the many genes being sequenced might represent a plausible explanation for a given case. We performed targeted gene panel analysis of 43 established neuromuscular disease genes in a patient with congenital fiber-type disproportion (CFTD) and fatal infantile cardiomyopathy. Initial review of variants identified changes in four genes that could be considered relevant candidates to cause this child's disease. Further analysis revealed that two of these are likely benign, but a homozygous frameshift variant in the myosin light chain 2 gene, MYL2, and a heterozygous nonsense mutation in the nebulin gene, NEB, met criteria to be classified as likely pathogenic or pathogenic. Recessive MYL2 mutations are a rare cause of CFTD associated with both skeletal and cardiomyopathy, whereas recessive NEB mutations cause nemaline myopathy. Although the proband's phenotype is likely largely explained by the MYL2 variant, the heterozygous pathogenic NEB variant cannot be ruled out as a contributing factor. This case illustrates the complexity when analyzing large numbers of variants from targeted gene panels in which each of the genes might plausibly contribute to the patient's clinical presentation.Entities:
Keywords: abnormality of the musculature of the limbs; dilated cardiomyopathy; generalized muscle weakness; generalized neonatal hypotonia; polyhydramnios; skeletal myopathy; type 1 fibers relatively smaller than type 2 fibers
Mesh:
Substances:
Year: 2019 PMID: 31127036 PMCID: PMC6672024 DOI: 10.1101/mcs.a004184
Source DB: PubMed Journal: Cold Spring Harb Mol Case Stud ISSN: 2373-2873
Figure 1.Microscopic examination substantiates the diagnosis of congenital fiber-type disproportion (CFTD). (A) Gomori trichrome staining does not reveal ragged red fibers or rimmed vacuoles. No definite nemaline rods are seen. Intramuscular nerve twigs are myelinated. (B) NAHD-TR-reacted sections reveal no cores, targetoid, or target fibers. Slight predominance of type 1 fibers is seen. Type 1 fibers are significantly smaller than type 2 fibers (mean type 2 fiber diameter-mean type 1 fiber diameter/mean type 2 fiber diameter = 40%). (C) ATPase (pH 9.4) staining reveals the slight predominance of type 1 fibers and type 1 fiber hypotrophy. (D) Electron microscopy (EM) does not show any evidence of nemaline bodies.
Variant table
| Gene | Chr | HGVS DNA reference | HGVS protein reference | Variant type | Predicted effect | dbSNP ID | Genotype | ClinVar ID |
|---|---|---|---|---|---|---|---|---|
| 12 | NM_000432.3: c.188del | NP_000423.2: p.(Asn63Metfs*7) | Deletion | Frameshift | rs1177936172 | Homozygous | NA | |
| 2 | NM_001271208.2: c.25435C>T | NP_001258137.2: p.(Gln8479*) | Substitution | Stop-gained | rs778104284 | Heterozygous | NA | |
| 2 | NM_001267550.2: c.33513_33515dup | NP_001254479.2: p.(Glu11172dup) | Duplication | Insertion | rs368327166 | Heterozygous | 46889 | |
| X | NM_004021.2: c.3669_3681del | NP_004012.1: p.(Asp1223Glufs*6) | Deletion | Frameshift | rs752332058 | Hemizygous | 201754 |
(Chr) Chromosome, (HGVS) Human Genome Variation Society, (NA) not available.
Figure 2.(A) DNA Sanger sequencing results of the proband (“P,” 1053-1, top tracing), mother (“M,” 1053-2), and father (“F,” 1053-3), illustrating the myosin light chain-2 (MYL2) c.188del p.(Asn63Metfs* 7) variant (arrowhead). Sequencing reads for parents are shown in both directions, demonstrating that they are heterozygous and proband homozygous for the mutation. (B) The proband (“P,” top) also has heterozygote truncating nebulin (NEB) mutation c.25435C>T p.(Gln8479*) (arrowhead). The father (“F,” bottom), but not the mother (“M,” middle) also carries this heterozygous variant.