ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.5033T>C (p.Val1678Ala)

gnomAD frequency: 0.00019  dbSNP: rs151337641
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000531415 SCV000623902 uncertain significance Chédiak-Higashi syndrome 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 1678 of the LYST protein (p.Val1678Ala). This variant is present in population databases (rs151337641, 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: 454486). 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 LYST 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.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002263730 SCV002543639 uncertain significance Autoinflammatory syndrome 2020-06-01 criteria provided, single submitter clinical testing
GenomeConnect - Invitae Patient Insights Network RCV000531415 SCV001749750 not provided Chédiak-Higashi syndrome no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 03-07-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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