ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.656T>C (p.Met219Thr)

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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 RCV002756811 SCV003027685 uncertain significance Chédiak-Higashi syndrome 2024-12-19 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 219 of the LYST protein (p.Met219Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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: 1984414). 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) indicates that this missense variant is not expected to disrupt LYST protein function with a negative predictive value of 80%. 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.
Ambry Genetics RCV002800259 SCV003670124 uncertain significance Inborn genetic diseases 2022-12-28 criteria provided, single submitter clinical testing The c.656T>C (p.M219T) alteration is located in exon 5 (coding exon 3) of the LYST gene. This alteration results from a T to C substitution at nucleotide position 656, causing the methionine (M) at amino acid position 219 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV002756811 SCV003815231 uncertain significance Chédiak-Higashi syndrome 2019-02-14 criteria provided, single submitter clinical testing

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