ClinVar Miner

Submissions for variant NM_001382567.1(STIM1):c.22G>A (p.Ala8Thr)

gnomAD frequency: 0.00001  dbSNP: rs751520286
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001338551 SCV001532231 uncertain significance Stormorken syndrome; Combined immunodeficiency due to STIM1 deficiency; Myopathy with tubular aggregates 2022-08-16 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1035654). This variant has not been reported in the literature in individuals affected with STIM1-related conditions. This variant is present in population databases (rs751520286, gnomAD 0.006%). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 8 of the STIM1 protein (p.Ala8Thr).
Revvity Omics, Revvity RCV003135998 SCV003818109 uncertain significance not provided 2022-03-14 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV003339603 SCV004046972 uncertain significance Immunodeficiency, common variable, 10 criteria provided, single submitter clinical testing The missense variant c.22G>A (p.Ala8Thr) in STIM1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has been reported to the ClinVar database as Uncertain Significance. The p.Ala8Thr variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.0007955% is reported in gnomAD. The amino acid Ala at position 8 is changed to a Thr changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by PolyPhen2 and the residue is conserved across species. The amino acid change p.Ala8Thr in STIM1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as uncertain significance .

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