ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.1993-1G>A

gnomAD frequency: 0.00003  dbSNP: rs369552114
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000420333 SCV000333995 pathogenic not provided 2017-01-30 criteria provided, single submitter clinical testing
Counsyl RCV000382987 SCV000486122 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2016-11-02 criteria provided, single submitter clinical testing
GeneDx RCV000420333 SCV000517213 pathogenic not provided 2024-01-30 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); This variant is associated with the following publications: (PMID: 15689361, 32528171, 10330340, 26404900, 18055493)
Fulgent Genetics, Fulgent Genetics RCV000763350 SCV000894040 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A; Muscular dystrophy, limb-girdle, autosomal dominant 4 2018-10-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000382987 SCV001218172 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2023-10-17 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 17 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 (rs369552114, gnomAD 0.003%). Disruption of this splice site has been observed in individuals with clinical features of autosomal recessive limb-girdle muscular dystrophy (PMID: 18055493; Invitae). ClinVar contains an entry for this variant (Variation ID: 282494). 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.
Revvity Omics, Revvity RCV000420333 SCV002018068 pathogenic not provided 2020-02-21 criteria provided, single submitter clinical testing
Natera, Inc. RCV000382987 SCV002085544 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2021-07-15 no assertion criteria provided clinical testing
Baylor Genetics RCV003475894 SCV004211564 pathogenic Muscular dystrophy, limb-girdle, autosomal dominant 4 2023-09-13 flagged submission clinical testing

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