ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.3235T>G (p.Ser1079Ala)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001911934 SCV002139542 uncertain significance Chédiak-Higashi syndrome 2024-10-16 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 1079 of the LYST protein (p.Ser1079Ala). This variant is not present in population databases (gnomAD no frequency). 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: 1376128). 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 RCV002552188 SCV003581617 uncertain significance Inborn genetic diseases 2021-09-16 criteria provided, single submitter clinical testing The c.3235T>G (p.S1079A) alteration is located in exon 6 (coding exon 4) of the LYST gene. This alteration results from a T to G substitution at nucleotide position 3235, causing the serine (S) at amino acid position 1079 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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