Small mutations in Duchenne/Becker muscular dystrophy in 164 unrelated Polish patients

Zimowski, Janusz; Purzycka, Joanna; Pawelec, Magdalena; Ozdarska, Katarzyna; Zaremba, Jacek

doi:10.1007/s13353-020-00605-0

Cited by 5 publications

(3 citation statements)

References 24 publications

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“…There are a number of studies reporting the functional analysis of several distinct splicing variants, but they do not provide a complete picture of the place of splicing variants in the structure of all pathogenic DMD variants. Most studies have focused on variants located at consensus positions of splice sites and have rarely explored exonic splicing variants (10, 68, 69). Moreover, when a newly identified variant is reported to affect splicing, it is often based solely on bioinformatics predictions without experimental confirmation (45, 70) In this study, we attempted to characterize the full spectrum of splicing variants in the DMD gene.…”

Section: Discussionmentioning

confidence: 99%

Revision of splicing variants in theDMDgene

Davydenko,

Filatova,

Skoblov

2024

Preprint

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Background: Pathogenic variants in the dystrophin (DMD) gene lead to X-linked recessive Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Nucleotide variants that affect splicing are a known cause of hereditary diseases. However, their representation in the public genomic variation databases is limited due to the low accuracy of their interpretation, especially if they are located within exons. The analysis of splicing variants in the DMD gene is essential both for understanding the underlying molecular mechanisms of the dystrophinopathies' pathogenesis and selecting suitable therapies for patients. Results: Using deep in silico mutagenesis of the entire DMD gene sequence and subsequent SpliceAI splicing predictions, we identified 7,948 DMD single nucleotide variants that could potentially affect splicing, 863 of them were located in exons. Next, we analyzed over 1,300 disease-associated DMD SNVs previously reported in the literature (373 exonic and 956 intronic) and intersected them with SpliceAI predictions. We predicted that ~95% of the intronic and ~10% of the exonic reported variants could actually affect splicing. Interestingly, the majority (75%) of patient-derived intronic variants were located in the AG-GT terminal dinucleotides of the introns, while these positions accounted for only 13% of all intronic variants predicted in silico. Of the 97 potentially spliceogenic exonic variants previously reported in patients with dystrophinopathy, we selected 38 for experimental validation. For this, we developed and tested a minigene expression system encompassing 27 DMD exons. The results showed that 35 (19 missense, 9 synonymous, and 7 nonsense) of the 38 DMD exonic variants tested actually disrupted splicing. We compared the observed consequences of splicing changes between variants leading to severe Duchenne and milder Becker muscular dystrophy and showed a significant difference in their distribution. This finding provides extended insights into relations between molecular consequences of splicing variants and the clinical features. Conclusions: Our comprehensive bioinformatics analysis, combined with experimental validation, improves the interpretation of splicing variants in the DMD gene. The new insights into the molecular mechanisms of pathogenicity of exonic single nucleotide variants contribute to a better understanding of the clinical features observed in patients with Duchenne and Becker muscular dystrophy.

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Section: Discussionmentioning

confidence: 99%

Revision of splicing variants in theDMDgene

Davydenko,

Filatova,

Skoblov

2024

Preprint

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“…This study highlights the challenges encountered in achieving an accurate genetic diagnosis for individuals with suspected Becker muscular dystrophy, particularly when dealing with deep intronic splice-altering variants ( Yang et al, 2019 ; Zimowski et al, 2021 ; Viggiano et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Case report: a novel deep intronic splice-altering variant in DMD as a cause of Becker muscular dystrophy

Berntsson,

Matsson,

Kristoffersson

et al. 2023

Front. Genet.

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We present the case of a male patient who was ultimately diagnosed with Becker muscular dystrophy (BMD; MIM# 300376) after the onset of muscle weakness in his teens progressively led to significant walking difficulties in his twenties. A genetic diagnosis was pursued but initial investigation revealed no aberrations in the dystrophin gene (DMD), although immunohistochemistry and Western blot analysis suggested the diagnosis of dystrophinopathy. Eventually, after more than 10 years, an RNA analysis captured abnormal splicing where 154 nucleotides from intron 43 were inserted between exon 43 and 44 resulting in a frameshift and a premature stop codon. Normal splicing of the DMD gene was also observed. Additionally, a novel variant c.6291–13537A>G in DMD was confirmed in the genomic DNA of the patient. The predicted function of the variant aligns with the mRNA results. To conclude, we here demonstrate that mRNA analysis can guide the diagnosis of non-coding genetic variants in DMD.

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“…Exon 70 and exon 22 mutations were more frequent in our findings. Although most studies have found that small mutations are evenly distributed throughout the DMD gene ( Zimowski et al, 2021 ), hot-spot mutation regions are deserved to be paid more attention, so that more efficient treatment targets can be discovered.…”

Section: Discussionmentioning

confidence: 99%

Clinical and genetic characteristics of Chinese Duchenne/Becker muscular dystrophy patients with small mutations

Gan

Liu²,

Yang³

et al. 2022

Front. Neurosci.

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BackgroundDuchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are amongst the inherited neuromuscular diseases with the highest incidence. Small mutations are less common and therefore have been poorly studied in China.Materials and methodsThe clinical data of 150 patients diagnosed with DMD/BMD by genetic analysis in Hunan Children’s Hospital from 2009 to 2021 were analyzed. The patients were followed up for an average of 3.42 years and their clinical characteristics were collected. Loss of ambulation (LOA) was used to evaluate the severity of disease progression. The correlation among clinical features, different variants, and glucocorticoid (GC) treatment was analyzed by Cox regression analysis.Results150 different variants were detected in this study, including 21 (14%) novel mutations, 88 (58.7%) non-sense mutations, 33 (22.0%) frameshift mutations, 22 (14.7%) splicing mutations, and 7 (4.7%) missense mutations. Single-exon skipping and single- or double-exon (double/single-exon) skipping strategies covered more than 90% of patients with small mutations. A case with frameshift mutation combined with Klinefelter’s syndrome (47, XXY) and another one with missense mutation combined with epilepsy was found in our study. De novo mutations accounted for 30.0% of all patients. The mean onset age was 4.19 ± 1.63 years old, and the mean diagnosed age was 5.60 ± 3.13 years old. The mean age of LOA was 10.4 years old (40 cases). 60.7% of them received GC treatment at 7.0 ± 2.7 years old. The main causes of complaints were muscle weakness, high creatine kinase (CK), motor retardation, and family history. The risk factors of LOA were positive family history (HR 5.52, CI 1.26–24.18), short GC treatment duration (HR 0.54, CI 0.36–0.82) and frameshift mutation (HR 14.58, CI 1.74–121.76). DMD patients who treated with GC after 7 years old had a higher risk of earlier LOA compared to those receiving treatment before the age of 7 (HR 0.083, CI 0.009–0.804). Moreover, an earlier onset age, a higher CK value, and a larger LOA population were found in the DMD patients compared to the BMD ones. Finally, the locations of the most frequent mutation were in exon 70 and exon 22.ConclusionIn conclusion, 150 small mutations were identified in this study, and 21 of them were discovered for the first time. We found the hotspots of small mutations were in exon 70 and exon 20. Also, the analysis showed that positive family history, frameshift mutation, short duration of GC treatment, and delayed GC treatment resulted in earlier LOA for the DMD patients. Taken together, our findings complement the mutation spectrum of DMD/BMD, benefit us understanding to the DMD disease, and lay foundations for the clinical trials.

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Small mutations in Duchenne/Becker muscular dystrophy in 164 unrelated Polish patients

Cited by 5 publications

References 24 publications

Revision of splicing variants in theDMDgene

Revision of splicing variants in theDMDgene

Case report: a novel deep intronic splice-altering variant in DMD as a cause of Becker muscular dystrophy

Clinical and genetic characteristics of Chinese Duchenne/Becker muscular dystrophy patients with small mutations

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