ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.499-1G>A

gnomAD frequency: 0.00006  dbSNP: rs863224964
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000201080 SCV000255666 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2014-08-08 criteria provided, single submitter clinical testing
Counsyl RCV000201080 SCV000798959 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2018-04-04 criteria provided, single submitter clinical testing
Invitae RCV000201080 SCV001395475 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2024-01-10 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 3 of the CAPN3 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 CAPN3 are known to be pathogenic (PMID: 10330340, 15689361). This variant is present in population databases (no rsID available, gnomAD 0.01%). Disruption of this splice site has been observed in individuals with autosomal recessive limb-girdle muscular dystrophy (PMID: 16650086, 18055493). ClinVar contains an entry for this variant (Variation ID: 217157). 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.
Baylor Genetics RCV003462349 SCV004213788 pathogenic Muscular dystrophy, limb-girdle, autosomal dominant 4 2023-04-07 criteria provided, single submitter clinical testing
Natera, Inc. RCV000201080 SCV001461306 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2020-09-16 no assertion criteria provided clinical testing

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