ClinVar Miner

Submissions for variant NM_000070.3(CAPN3):c.2306G>A (p.Arg769Gln)

gnomAD frequency: 0.00014  dbSNP: rs80338802
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000711017 SCV000331919 pathogenic not provided 2018-09-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000020096 SCV000766725 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2025-01-06 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 769 of the CAPN3 protein (p.Arg769Gln). This variant is present in population databases (rs80338802, gnomAD 0.006%). This missense change has been observed in individuals with autosomal recessive limb-girdle muscular dystrophy (PMID: 7720071, 7762565, 7795603, 9246005, 12461690, 14645990). It is commonly reported in individuals of Amish ancestry (PMID: 9246005). ClinVar contains an entry for this variant (Variation ID: 17613). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CAPN3 protein function. Experimental studies have shown that this missense change affects CAPN3 function (PMID: 9642272). For these reasons, this variant has been classified as Pathogenic.
Athena Diagnostics RCV000711017 SCV000841335 pathogenic not provided 2018-03-22 criteria provided, single submitter clinical testing
Kariminejad - Najmabadi Pathology & Genetics Center RCV001814000 SCV001755555 pathogenic Abnormality of the musculature 2021-07-10 criteria provided, single submitter clinical testing
GeneDx RCV000711017 SCV001764949 pathogenic not provided 2019-12-09 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 31980526, 32668095, 31028937, 7762565, 7795603, 9642272, 14645990, 18258189, 19015733, 20301490, 28300015, 25252238, 16650086, 12461690, 9246005, 7720071, 30564623, 23553538)
Revvity Omics, Revvity RCV000711017 SCV002018045 pathogenic not provided 2022-12-08 criteria provided, single submitter clinical testing
Baylor Genetics RCV003473106 SCV004211569 pathogenic Muscular dystrophy, limb-girdle, autosomal dominant 4 2024-03-15 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000711017 SCV005414255 pathogenic not provided 2024-04-08 criteria provided, single submitter clinical testing PP1, PP3, PM2, PM3, PS4
Fulgent Genetics, Fulgent Genetics RCV005007872 SCV005637817 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A; Muscular dystrophy, limb-girdle, autosomal dominant 4 2024-06-05 criteria provided, single submitter clinical testing
OMIM RCV000020096 SCV000039467 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 1997-07-01 no assertion criteria provided literature only
GeneReviews RCV000020096 SCV000040414 not provided Autosomal recessive limb-girdle muscular dystrophy type 2A no assertion provided literature only
Counsyl RCV000020096 SCV000788465 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2017-04-21 no assertion criteria provided clinical testing
Natera, Inc. RCV000020096 SCV001456375 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2A 2020-09-16 no assertion criteria provided clinical testing

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