ClinVar Miner

Submissions for variant NM_001382567.1(STIM1):c.58G>A (p.Gly20Ser)

dbSNP: rs2135170451
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002032122 SCV002313340 uncertain significance Stormorken syndrome; Combined immunodeficiency due to STIM1 deficiency; Myopathy with tubular aggregates 2022-09-23 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 STIM1 protein function. ClinVar contains an entry for this variant (Variation ID: 1524986). This variant has not been reported in the literature in individuals affected with STIM1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 20 of the STIM1 protein (p.Gly20Ser).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003479392 SCV004222832 uncertain significance not specified 2023-11-17 criteria provided, single submitter clinical testing Variant summary: STIM1 c.58G>A (p.Gly20Ser) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251412 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.58G>A in individuals affected with STIM1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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