ClinVar Miner

Submissions for variant NM_001130987.2(DYSF):c.2864+1G>A

gnomAD frequency: 0.00001  dbSNP: rs199954546
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Clinical Genetics and Genomics, Karolinska University Hospital RCV000512137 SCV000607738 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2B 2017-10-11 criteria provided, single submitter clinical testing ACMG: +PVS1 +PM2 +PP3
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000512137 SCV000746544 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2B 2020-05-03 criteria provided, single submitter clinical testing
Counsyl RCV000512137 SCV000796693 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2B 2017-12-22 criteria provided, single submitter clinical testing
Invitae RCV001217776 SCV001389628 pathogenic Qualitative or quantitative defects of dysferlin 2023-11-06 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 26 of the DYSF gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in DYSF are known to be pathogenic (PMID: 17698709, 20301480). This variant is present in population databases (rs199954546, gnomAD 0.002%). Disruption of this splice site has been observed in individual(s) with dysferlinopathy (PMID: 17994539, 18853459, 26000923). This variant is also known as IVS26+1G>A. ClinVar contains an entry for this variant (Variation ID: 443997). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV002286745 SCV002577127 pathogenic not provided 2022-03-10 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Identified in an individual with Miyoshi myopathy in published literature who also harbored a second DYSF variant in trans (Chakravorty et al., 2021); This variant is associated with the following publications: (PMID: 27602406, 31589614, 33610434, 33726816, 26000923, 22213072, Chakravorty2021[Preprint], 18853459)
Baylor Genetics RCV001263253 SCV004194188 pathogenic Miyoshi muscular dystrophy 1 2023-10-06 criteria provided, single submitter clinical testing
Neuromuscular Department, Shariati Hospital, Tehran University of Medical Sciences RCV001263253 SCV001441253 pathogenic Miyoshi muscular dystrophy 1 2020-10-23 no assertion criteria provided clinical testing Since age of 15, the patient developed bilateral foot plantar flexion weakness, difficulty climbing upstairs and some wasting of calf muscles. CK had been elevated and the EMG was myopathic.

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