ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.10345C>T (p.Arg3449Ter)

dbSNP: rs754616030
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000300771 SCV000330617 likely pathogenic not provided 2019-09-05 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV001381378 SCV001579748 pathogenic Chédiak-Higashi syndrome 2024-03-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg3449*) in the LYST gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LYST are known to be pathogenic (PMID: 9215679, 11857544). This variant is present in population databases (rs754616030, 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: 280681). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV001381378 SCV004191160 likely pathogenic Chédiak-Higashi syndrome 2023-12-15 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001381378 SCV005642595 likely pathogenic Chédiak-Higashi syndrome 2024-02-15 criteria provided, single submitter clinical testing

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