ClinVar Miner

Submissions for variant NM_000232.5(SGCB):c.346A>G (p.Met116Val)

dbSNP: rs752168132
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000407437 SCV000338206 uncertain significance not provided 2015-12-07 criteria provided, single submitter clinical testing
3billion RCV002250615 SCV002521661 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2E 2022-05-22 criteria provided, single submitter clinical testing Amino acid change identical to known pathogenic variant has been previously reported with supporting evidence; this might be considered evidence of a supporting level (PMID:33250842). It has been reported with an extremely low frequency in the gnomAD v2.1.1 (https://gnomad.broadinstitute.org/) dataset. In silico prediction tools and conservation analysis predicted that this variant was probably damaging to the protein structure/function (REVEL: 0.864>=0.6). herefore, this variant is classified as uncertain significanceaccording to the recommendation of ACMG/AMP guideline.
Revvity Omics, Revvity RCV002250615 SCV004238649 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2E 2023-10-02 criteria provided, single submitter clinical testing
Invitae RCV002250615 SCV004483568 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2E 2023-06-29 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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 SGCB protein function. ClinVar contains an entry for this variant (Variation ID: 285260). This missense change has been observed in individual(s) with clinical features of limb-girdle muscular dystrophy and/or muscular dystrophy (PMID: 31069529, 33250842; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs752168132, gnomAD 0.003%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 116 of the SGCB protein (p.Met116Val).

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