A six-year-old Taiwanese boy with unexplained muscle weakness and a creatine kinase level nearly 20,000 units per liter has led researchers to identify a previously unreported mutation associated with Duchenne muscular dystrophy (DMD). The genetic change, a two-nucleotide deletion in the DMD gene, was found through whole-exome sequencing and is predicted to produce a severely shortened form of dystrophin, the protein whose absence or dysfunction causes the progressive muscle degeneration characteristic of the disease. The case, reported in Molecular Genetics & Genomic Medicine, expands the known mutational spectrum of DMD and illustrates how genomic sequencing, evolutionary comparisons and protein-structure modeling can be combined when laboratory tests cannot directly measure the effect of a new mutation.
DMD is an X-linked neuromuscular disorder that primarily affects boys because they have only one X chromosome. The DMD gene is one of the largest in the human genome and contains the instructions for dystrophin, a giant cytoskeletal protein that helps connect the internal actin network of muscle cells to the extracellular matrix through the dystrophin-associated protein complex. This molecular bridge acts like a shock absorber and stabilizing support during repeated contraction. When dystrophin is absent or defective, the membrane surrounding muscle fibers becomes vulnerable to mechanical stress. Repeated contractions can then trigger membrane damage, inflammation and progressive loss of muscle tissue. Although large deletions account for most disease-causing DMD variants, smaller substitutions, duplications, insertions, inversions and frameshift mutations can also disrupt the gene.
The child described in the report had several features that could have delayed recognition of a neuromuscular disorder. He had a history of low muscle tone, mild gross-motor delay, attention-deficit/hyperactivity disorder and autistic traits, and had already been receiving rehabilitation therapy. His acute presentation was also unusual: abdominal discomfort and intermittent chest pain brought him to an emergency department. Routine laboratory testing, however, revealed a creatine kinase concentration of 19,061 U/L. Creatine kinase is an enzyme released into the bloodstream when muscle fibers are damaged, and such a dramatic elevation is a powerful warning sign for muscular dystrophy or another muscle disease. Liver enzymes and lactate dehydrogenase were also high, but cardiac markers, urine testing and kidney function were normal, making an acute cardiac or systemic cause less likely. In the absence of dark urine or strenuous exercise, rhabdomyolysis was considered less probable.
A targeted neurological examination then revealed more characteristic signs of DMD. The boy had a positive Gowers’ sign, using his hands to push against his legs or the floor while rising, as well as mild inward curvature of the lower back and a broad, waddling gait. He could stand on one foot but could not hop, suggesting that high-demand movements were already exposing weakness despite preserved independent walking. Nerve-conduction studies were normal, as is often expected in a primary muscle disorder, and electromyography was not performed because of tactile hypersensitivity. His creatine kinase level remained elevated at 7,736 U/L after discharge and measured 8,440 U/L one month later. At that follow-up, his North Star Ambulatory Assessment score was 26 out of 34, consistent with an early ambulatory stage in which children may walk independently while beginning to lose performance in more demanding motor tasks. Prednisolone therapy was started for suspected DMD.
Whole-exome sequencing, which reads the protein-coding regions of thousands of genes simultaneously, identified a hemizygous variant in DMD: NM_004006.3:c.6050_6051del, corresponding to p.Leu2017Profs*5. “Hemizygous” means that, in this boy’s single X-linked copy of the gene, the variant was present without a normal second copy to compensate. The deletion shifts the genetic reading frame and introduces a premature stop signal after only five altered amino acids. Such frameshifts can cause the cell to destroy the abnormal messenger RNA through nonsense-mediated decay, or they can produce a truncated protein that is unstable or unable to perform its normal role. Sanger sequencing confirmed that the variant arose de novo in the child and was not detected in either parent, including his mother, who could have carried an X-linked mutation without symptoms. The variant was absent from ClinVar, the Taiwan BioBank and the Genome Aggregation Database, emphasizing why newly discovered mutations can be difficult to classify using databases alone.
Under guidelines from the American College of Medical Genetics and Genomics, the researchers classified the variant as likely pathogenic. Their interpretation relied chiefly on two lines of evidence. The first was PVS1, very strong evidence that a predicted loss-of-function variant is damaging in a gene where loss of function causes disease. The second was PS2, evidence that the variant occurred de novo in a patient with a phenotype consistent with the disorder. Additional computational evidence, designated PP3, came from conservation and structural analyses. The mutation lies in exon 42, which encodes part of the 16th spectrin-like repeat within dystrophin’s central rod domain. Spectrin-like repeats are compact structural modules built around a three-helix bundle. In dystrophin, the central rod functions as an elastic spacer and mechanical buffer, helping the protein tolerate the forces generated when muscle fibers contract.
The deleted nucleotides occupy a region that has remained strikingly similar across many vertebrate species. In the researchers’ comparative analysis, both positions received phastCons scores of 1, indicating a very high probability that they belong to a conserved genomic element. Their phyloP scores were +2.925 and +1.015, values consistent with evolutionary constraint at the nucleotide level. Alignments across nine vertebrates, from chimpanzees to lizards, suggested partial conservation, although the pattern was not seen in avian sequences and fish were not represented in the browser data used for the comparison. The sequencing data itself showed more than 30-fold average coverage at the site, providing technical support for the call. Conservation does not prove that a mutation causes disease, but it can indicate that a sequence has been preserved because it performs an important biological function.
To explore what the mutation might do to the protein, the team modeled a dystrophin fragment spanning residues Val1401 to Leu2800 using an AlphaFold-derived structure and introduced the frameshift computationally. The predicted mutant appeared less able to preserve the characteristic three-helix bundle around the affected spectrin-like repeat than the modeled normal protein. The site had a predicted local distance difference test, or pLDDT, score of 92.52, suggesting high confidence in the structure predicted for that region, while IUPred2A estimated a low intrinsic-disorder probability of 0.13. The affected segment therefore appears to be an ordered structural element rather than a flexible, unstructured tail. The mutation is also present in nine of 15 dystrophin isoforms identified in the analysis, including Dp427m, the major full-length isoform in skeletal muscle. Using the CHARMM force field, the researchers calculated relative potential energies for the normal and mutant models and compared them with known exon 42 variants. The new frameshift showed a destabilization pattern resembling two previously reported pathogenic frameshifts, whereas likely benign missense changes caused minimal shifts relative to the normal model.
The investigators stress that these results are supportive rather than definitive. Energy calculations sum estimated bonded and non-bonded interactions, including bond, angle, dihedral, van der Waals and electrostatic terms, but they do not reproduce the full dynamics of a living muscle cell. AlphaFold predictions are also not fully validated for proteins altered by frameshifts and premature truncation. The study did not include a muscle biopsy, dystrophin quantification, western blotting or patient-derived muscle-cell experiments that could directly demonstrate loss of protein or membrane instability. Even so, the case highlights the practical value of combining genomic data with structure-informed analysis when a child has a strongly suggestive clinical picture but carries a mutation not yet listed in major databases. It also underscores the importance of testing children with unexplained motor abnormalities and very high creatine kinase levels, even when developmental or behavioral diagnoses appear to offer another explanation. In this case, diagnosis during the early ambulatory phase created an opportunity for treatment and counseling, while the precise genetic result may also guide eligibility for future therapies. The identified mutation is not amenable to currently approved exon-skipping treatments, but documenting it adds an essential piece to the broader map of DMD biology and may help refine molecular diagnosis as disease-modifying options continue to expand.
Subject of Research: A novel DMD frameshift variant and its clinical, evolutionary and structural implications in Duchenne muscular dystrophy
Subject of Research: Biology
Article Title: Novel DMD Frameshift Variant (p.Leu2017Profs*5) in Spectrin-Like Repeat 16 Expands the Mutational Spectrum of DMD
Article References: Lin, Y.-C., Luxton, G. W. G., Lee, H.-J., Lu, Y.-Y., Yang, H.-C., Hung, K.-S., Lai, M.-T., & Hu, C.-F. (2026). Novel DMD Frameshift Variant (p.Leu2017Profs*5) in Spectrin‐Like Repeat 16 Expands the Mutational Spectrum of DMD. Molecular Genetics & Genomic Medicine, 14(7), Article e70257. https://doi.org/10.1002/mgg3.70257
Image Credits: AI Generated
DOI: 10.1002/mgg3.70257
Keywords: Duchenne muscular dystrophy, DMD gene, frameshift variant, dystrophin, whole-exome sequencing, AlphaFold modeling, spectrin-like repeat, genetic diagnosis
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SCIENMAG. (August 28, 2026). Novel DMD Frameshift Variant in Spectrin-Like Repeat 16 Expands Mutation Spectrum. https://scienmag.com/novel-dmd-frameshift-variant-in-spectrin-like-repeat-16-expands-mutation-spectrum/
SCIENMAG. “Novel DMD Frameshift Variant in Spectrin-Like Repeat 16 Expands Mutation Spectrum.” Scienmag, 28 August 2026, https://scienmag.com/novel-dmd-frameshift-variant-in-spectrin-like-repeat-16-expands-mutation-spectrum/. Accessed 28 August 2026.
SCIENMAG. “Novel DMD Frameshift Variant in Spectrin-Like Repeat 16 Expands Mutation Spectrum.” Scienmag. August 28, 2026. https://scienmag.com/novel-dmd-frameshift-variant-in-spectrin-like-repeat-16-expands-mutation-spectrum/
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