ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.6185G>A (p.Gly2062Glu)

gnomAD frequency: 0.00004  dbSNP: rs756651685
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768016 SCV000898808 uncertain significance Chédiak-Higashi syndrome 2021-03-30 criteria provided, single submitter clinical testing LYST NM_000081.3 exon 22 p.Gly2062Glu (c.6185G>A): This variant has not been reported in the literature but is present in 2/111072 European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs756651685). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Labcorp Genetics (formerly Invitae), Labcorp RCV000768016 SCV001533244 uncertain significance Chédiak-Higashi syndrome 2021-08-28 criteria provided, single submitter clinical testing This sequence change replaces glycine with glutamic acid at codon 2062 of the LYST protein (p.Gly2062Glu). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and glutamic acid. This variant is present in population databases (rs756651685, ExAC 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: 625976). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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 RCV002261200 SCV002541721 uncertain significance not provided 2021-04-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV002533932 SCV003533890 uncertain significance Inborn genetic diseases 2022-11-21 criteria provided, single submitter clinical testing The c.6185G>A (p.G2062E) alteration is located in exon 22 (coding exon 20) of the LYST gene. This alteration results from a G to A substitution at nucleotide position 6185, causing the glycine (G) at amino acid position 2062 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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