ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.8779A>T (p.Ile2927Phe)

gnomAD frequency: 0.00010  dbSNP: rs554841002
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002262049 SCV002543672 uncertain significance Autoinflammatory syndrome 2020-11-16 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002488657 SCV002790796 uncertain significance Chédiak-Higashi syndrome 2022-02-09 criteria provided, single submitter clinical testing
Invitae RCV002488657 SCV003525621 uncertain significance Chédiak-Higashi syndrome 2022-08-01 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 2927 of the LYST protein (p.Ile2927Phe). This variant is present in population databases (rs554841002, gnomAD 0.09%). 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: 1694327). 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: "Possibly 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.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV002488657 SCV003920172 uncertain significance Chédiak-Higashi syndrome 2022-03-18 criteria provided, single submitter clinical testing This variant has not been reported in the literature but is present in 0.08% (25/30610) of South Asian alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/1-235896825-T-A?dataset=gnomad_r2_1). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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