ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.7690G>A (p.Ala2564Thr)

gnomAD frequency: 0.00004  dbSNP: rs759733310
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001880448 SCV002120894 uncertain significance Chédiak-Higashi syndrome 2022-07-26 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 2564 of the LYST protein (p.Ala2564Thr). This variant is present in population databases (rs759733310, gnomAD 0.003%). 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: 1356549). 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.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002264402 SCV002543661 uncertain significance Autoinflammatory syndrome 2019-12-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002545847 SCV003637772 uncertain significance Inborn genetic diseases 2022-08-08 criteria provided, single submitter clinical testing The c.7690G>A (p.A2564T) alteration is located in exon 28 (coding exon 26) of the LYST gene. This alteration results from a G to A substitution at nucleotide position 7690, causing the alanine (A) at amino acid position 2564 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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