ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.245C>T (p.Pro82Leu)

gnomAD frequency: 0.00004  dbSNP: rs886042478
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000489536 SCV000334423 pathogenic not provided 2018-07-11 criteria provided, single submitter clinical testing
GeneDx RCV000489536 SCV000577327 likely pathogenic not provided 2024-10-02 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 12461690, 12890817, 15689361, 16100770, 16141003, 15221789, 16372320, 15351423, 20635405, 14981715, 27023906, 17157502, 31980526, 31862442, 27447704, 26886200, 29970176, 35157181, 25135358, 31555977, 35894554, 36385624, 37526466, 32528171)
Athena Diagnostics RCV000489536 SCV000612642 pathogenic not provided 2016-10-04 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000311426 SCV000830891 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2023-12-14 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 82 of the CAPN3 protein (p.Pro82Leu). This variant is present in population databases (no rsID available, gnomAD 0.003%). This missense change has been observed in individual(s) with autosomal recessive limb-girdle muscular dystrophy (PMID: 12461690, 12890817, 15221789, 15351423, 16100770, 16141003, 16372320, 17157502, 20635405, 25135358, 26886200, 27447704). ClinVar contains an entry for this variant (Variation ID: 282783). 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 CAPN3 protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV000489536 SCV001246423 pathogenic not provided 2018-08-01 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000489536 SCV001446731 likely pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000489536 SCV002018075 pathogenic not provided 2022-10-01 criteria provided, single submitter clinical testing
Baylor Genetics RCV003475897 SCV004211531 pathogenic Muscular dystrophy, limb-girdle, autosomal dominant 4 2024-03-25 criteria provided, single submitter clinical testing
Counsyl RCV000311426 SCV000788754 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2016-12-15 no assertion criteria provided clinical testing

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