ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.2105C>T (p.Ala702Val)

gnomAD frequency: 0.00001  dbSNP: rs886042557
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000725206 SCV000334984 likely pathogenic not provided 2015-09-15 criteria provided, single submitter clinical testing
Counsyl RCV000311834 SCV000794103 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2017-09-13 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000311834 SCV001394807 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2024-01-03 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 702 of the CAPN3 protein (p.Ala702Val). This variant is present in population databases (no rsID available, gnomAD 0.002%). This missense change has been observed in individuals with autosomal recessive limb-girdle muscular dystrophy (PMID: 9150160, 16141003, 17236769, 27234031, 27262448, 30056071). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 283099). 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.
GeneDx RCV000725206 SCV001765281 likely pathogenic not provided 2023-03-24 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30056071, 27234031, 10330340, 9150160, 19556129, 16411092, 16650086, 15757244, 9266733, 27262448, 17994539, 17236769, 16141003, 35741838)
Baylor Genetics RCV003475900 SCV004211541 pathogenic Muscular dystrophy, limb-girdle, autosomal dominant 4 2024-02-26 criteria provided, single submitter clinical testing

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