ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.379+3A>G

gnomAD frequency: 0.00001  dbSNP: rs1164215001
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001774552 SCV002002010 uncertain significance not provided 2020-02-11 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports a deleterious effect on splicing; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV002512158 SCV003486404 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2024-10-16 criteria provided, single submitter clinical testing This sequence change falls in intron 2 of the CAPN3 gene. It does not directly change the encoded amino acid sequence of the CAPN3 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant has been observed in individuals with autosomal recessive limb-girdle muscular dystrophy (PMID: 34697879). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1315302). Studies have shown that this variant alters CAPN3 gene expression (PMID: 34697879). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in activation of a cryptic splice site, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 34697879). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV004571079 SCV005059993 pathogenic Muscular dystrophy, limb-girdle, autosomal dominant 4 2024-02-14 criteria provided, single submitter clinical testing
Rare Diseases Genetics and Genomics, Islamia College Peshawar RCV002512158 SCV002822846 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2021-04-23 no assertion criteria provided research

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