ClinVar Miner

Submissions for variant NM_004006.3(DMD):c.1649G>A (p.Arg550His)

gnomAD frequency: 0.00001  dbSNP: rs1424295439
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001240010 SCV001412926 uncertain significance Duchenne muscular dystrophy 2024-01-02 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 550 of the DMD protein (p.Arg550His). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with DMD-related conditions. ClinVar contains an entry for this variant (Variation ID: 965534). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt DMD protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV001576757 SCV001804009 uncertain significance not provided 2020-09-11 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variant in a gene in which most reported pathogenic variants are truncating/loss-of-function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004034634 SCV005021399 uncertain significance Cardiovascular phenotype 2023-10-20 criteria provided, single submitter clinical testing The p.R550H variant (also known as c.1649G>A), located in coding exon 14 of the DMD gene, results from a G to A substitution at nucleotide position 1649. The arginine at codon 550 is replaced by histidine, an amino acid with highly similar properties. Based on data from gnomAD, the A allele has an overall frequency of 0.0015% (3/204512) total alleles studied, with no hemizygote(s) observed. The highest observed frequency was 0.0054% (1/18561) of Finnish alleles. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001834111 SCV002090339 uncertain significance Becker muscular dystrophy; Duchenne muscular dystrophy; Cardiomyopathy; Dystrophin deficiency 2020-04-21 no assertion criteria provided clinical testing

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