ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.4513A>G (p.Ile1505Val)

gnomAD frequency: 0.00011  dbSNP: rs756527927
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000996124 SCV001150606 uncertain significance not provided 2017-09-01 criteria provided, single submitter clinical testing
Invitae RCV001057304 SCV001221789 uncertain significance Chédiak-Higashi syndrome 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1505 of the LYST protein (p.Ile1505Val). This variant is present in population databases (rs756527927, gnomAD 0.02%). 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: 807915). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000996124 SCV001715408 uncertain significance not provided 2020-01-31 criteria provided, single submitter clinical testing
GeneDx RCV000996124 SCV004012305 uncertain significance not provided 2023-01-09 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function

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