ClinVar Miner

Submissions for variant NM_001382567.1(STIM1):c.1681C>T (p.Arg561Cys)

gnomAD frequency: 0.00005  dbSNP: rs142239530
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000532168 SCV000634538 uncertain significance Stormorken syndrome; Combined immunodeficiency due to STIM1 deficiency; Myopathy with tubular aggregates 2025-01-23 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 530 of the STIM1 protein (p.Arg530Cys). This variant is present in population databases (rs142239530, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with STIM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 461723). 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 STIM1 protein function. 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.
Undiagnosed Diseases Network, NIH RCV000626054 SCV000746676 likely pathogenic Stormorken syndrome 2016-04-18 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV001508662 SCV001714962 uncertain significance not provided 2019-07-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV005278593 SCV005945339 uncertain significance Inborn genetic diseases 2025-02-22 criteria provided, single submitter clinical testing The c.1588C>T (p.R530C) alteration is located in exon 12 (coding exon 12) of the STIM1 gene. This alteration results from a C to T substitution at nucleotide position 1588, causing the arginine (R) at amino acid position 530 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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