ClinVar Miner

Submissions for variant NM_006949.4(STXBP2):c.1225C>T (p.Leu409Phe)

gnomAD frequency: 0.00001  dbSNP: rs763024326
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Total submissions: 2
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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 RCV002208785 SCV002495977 uncertain significance Familial hemophagocytic lymphohistiocytosis 5 2021-07-26 criteria provided, single submitter clinical testing STXBP2 NM_006949.3 exon 14 p.Leu409Phe (c.1225C>T): This variant has not been reported in the literature but is present in 0.02% (1/4834) of South Asian alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/19-7644731-C-T?dataset=gnomad_r3). Evolutionary conservation suggests that this variant may impact the protein; 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 RCV002208785 SCV002983232 uncertain significance Familial hemophagocytic lymphohistiocytosis 5 2022-06-05 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 409 of the STXBP2 protein (p.Leu409Phe). This variant is present in population databases (rs763024326, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with STXBP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1675137). 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.

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