ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.11116T>A (p.Cys3706Ser)

gnomAD frequency: 0.00001  dbSNP: rs1481260242
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001216864 SCV001388681 uncertain significance Chédiak-Higashi syndrome 2022-06-10 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with serine, which is neutral and polar, at codon 3706 of the LYST protein (p.Cys3706Ser). This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with LYST-related conditions. ClinVar contains an entry for this variant (Variation ID: 946076). 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: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
GeneDx RCV001760199 SCV001998917 uncertain significance not provided 2019-09-16 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; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV001216864 SCV003815306 uncertain significance Chédiak-Higashi syndrome 2019-11-19 criteria provided, single submitter clinical testing

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