Submissions for variant NM_004006.3(DMD):c.9225-647A>G

dbSNP: rs398124091

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000080835	SCV000112737	pathogenic	not provided	2014-04-29	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000179616	SCV000625984	pathogenic	Duchenne muscular dystrophy	2024-03-16	criteria provided, single submitter	clinical testing	This sequence change falls in intron 62 of the DMD gene. It does not directly change the encoded amino acid sequence of the DMD protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant has been observed in individual(s) with Becker muscular dystrophy (PMID: 14659407, 19602481, 23536893, 34297739; Invitae). ClinVar contains an entry for this variant (Variation ID: 94837). Studies have shown that this variant results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 14659407, 19602481, 23536893). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Illumina Laboratory Services, Illumina	RCV001270853	SCV001451625	likely pathogenic	Qualitative or quantitative defects of dystrophin	2019-02-13	criteria provided, single submitter	clinical testing	The DMD c.9225-647A>G variant is an intronic variant that has been reported in a hemizygous state in two unrelated individuals with Becker muscular dystrophy, one of whom also exhibited intellectual disability (Daoud et al. 2009; Juan-Mateu et al. 2013). A third individual with Becker muscular dystrophy and intellectual disability was reported to have an A>G nucleotide change in intron 62 that led to aberrant splicing and out-of-frame insertion of 67 nucleotides; however, the variant identified could not be confirmed as c.9225-647A>G (Béroud et al. 2004). In two of these reported cases, the variant was shown to have been inherited from the mother. The c.9225-647A>G variant was absent from the X chromosomes of 1200 normal controls and is absent from the Genome Aggregation Database in a region of adequate coverage for genomes. This region is not covered in exome sequencing. Multiple in silico tools predict this nucleotide change affects splicing, and RT-PCR analysis of RNA isolated from all affected patients has demonstrated that the variant results in aberrant use of a cryptic splice site, out-of-frame pseudoexon inclusion, and a prematurely truncated transcript. Semi-quantitative analysis suggested the abnormal transcript dominated expression over the full-length form, consistent with reduced dystrophin protein expression observed in patient muscle biopsy. Based on the collective evidence, the c.9225-647A>G variant is classified as likely pathogenic for dystrophinopathy.
GeneDx	RCV000080835	SCV002504145	pathogenic	not provided	2024-06-11	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect, as RT-PCR of patient muscle shows the variant causes a cryptic 5' splice site activation, leading to an abnormal transcript in the presence of residual wild type transcript (PMID: 19602481, 23536893); No data available from control populations to assess the frequency of this variant; This variant is associated with the following publications: (PMID: 23536893, 14659407, 19602481, 17041906, 32176650, Kumaraku2022[Article], 19367636, 28597072, 35165973, 34297739)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001270853	SCV002571930	pathogenic	Qualitative or quantitative defects of dystrophin	2022-08-10	criteria provided, single submitter	clinical testing	Variant summary: DMD c.9225-647A>G is located deep within intron 62, far from canonical splice sites. However, several computational tools predict a significant impact on normal splicing: Four predict the variant strengthens a cryptic 5' donor site. Several publications have given experimental evidence confirming that this variant affects mRNA splicing, which results in a frameshift caused by inclusion of a 67nt pseudoexon (e.g. Daoud_2009, Juan-Mateu_2013). The variant was absent in 21957 control chromosomes (gnomAD), and c.9225-647A>G has been reported in the literature in individuals affected with Duchenne Muscular Dystrophy, and Becker's Muscular Dystrophy with some reports of cognitive impairment (e.g.Deburgrave_2007, Daoud_2009, Juan-Mateu_2013, Yun_2021, Waldrop_2022). These data indicate that the variant is likely to be associated with disease. Western blot analysis of patient muscle biopsies have shown that the variant causes weak/trace levels of the Dystrophin protein, including complete loss of one specific DMD product, Dp71 (Daoud_2009). Four ClinVar submitters have assessed the variant since 2014: all classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.