ClinVar Miner

Submissions for variant NM_001130987.2(DYSF):c.5830C>T (p.Arg1944Ter)

gnomAD frequency: 0.00001  dbSNP: rs121908959
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000080312 SCV000335577 pathogenic not provided 2015-09-22 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000080312 SCV000613217 pathogenic not provided 2023-03-07 criteria provided, single submitter clinical testing This variant is expected to result in the loss of a functional protein. The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). In multiple individuals with Miyoshi muscular dystrophy, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. This variant is a common founder originating from Sueca, Spain (PMID: 16087766).
GeneDx RCV000080312 SCV000680751 pathogenic not provided 2023-03-24 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 16010686, 32400077, 33250842, 33215690, 30919934, 33715265, 31069529, 34559919, 33348118, 33610434, 20558759, 16087766)
Labcorp Genetics (formerly Invitae), Labcorp RCV000808564 SCV000948676 pathogenic Qualitative or quantitative defects of dysferlin 2024-05-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1905*) in the DYSF gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DYSF are known to be pathogenic (PMID: 17698709, 20301480). This variant is present in population databases (rs121908959, gnomAD 0.003%). This premature translational stop signal has been observed in individuals with dysferlinopathy (PMID: 16087766). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 6676). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000080312 SCV002021876 pathogenic not provided 2023-12-13 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003114177 SCV003800937 pathogenic Autosomal recessive limb-girdle muscular dystrophy 2023-01-16 criteria provided, single submitter clinical testing Variant summary: DYSF c.5713C>T (p.Arg1905X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic within ClinVar (e.g. c.5938A>T [p.Lys1980Ter], c.5953_5956del [p.Gln1985fs]). The variant allele was found at a frequency of 1.2e-05 in 251484 control chromosomes (gnomAD). c.5713C>T has been reported in the literature as a biallelic genotype in multiple individuals affected with Limb-Girdle Muscular Dystrophy or Miyoshi Myopathy (e.g. Vilchez_2005, Park_2012, Ankala_2014, Izumi_2015). These data indicate that the variant is very likely to be associated with disease. Seven ClinVar submitters have assessed the variant since 2014: all have classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Baylor Genetics RCV000007061 SCV004194157 pathogenic Miyoshi muscular dystrophy 1 2023-11-14 criteria provided, single submitter clinical testing
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre RCV000007063 SCV004808129 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2B 2024-03-29 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005025022 SCV005659345 pathogenic Miyoshi muscular dystrophy 1; Autosomal recessive limb-girdle muscular dystrophy type 2B; Distal myopathy with anterior tibial onset 2024-02-19 criteria provided, single submitter clinical testing
OMIM RCV000007061 SCV000027257 pathogenic Miyoshi muscular dystrophy 1 2005-08-01 no assertion criteria provided literature only
OMIM RCV000007062 SCV000027258 pathogenic Distal myopathy with anterior tibial onset 2005-08-01 no assertion criteria provided literature only
Counsyl RCV000007063 SCV000788443 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2B 2017-04-21 no assertion criteria provided clinical testing
OMIM RCV000007063 SCV000809055 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2B 2005-08-01 no assertion criteria provided literature only
GeneReviews RCV000007061 SCV001981616 not provided Miyoshi muscular dystrophy 1 no assertion provided literature only Founder variant in Spain
Natera, Inc. RCV000007063 SCV002080337 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2B 2020-10-22 no assertion criteria provided clinical testing

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