ClinVar Miner

Submissions for variant NM_006949.4(STXBP2):c.1393C>T (p.Arg465Cys)

gnomAD frequency: 0.00012  dbSNP: rs542557411
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000647330 SCV000769120 likely benign Familial hemophagocytic lymphohistiocytosis 5 2024-12-15 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000647330 SCV002814037 uncertain significance Familial hemophagocytic lymphohistiocytosis 5 2021-11-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004526731 SCV005039869 uncertain significance not specified 2024-03-18 criteria provided, single submitter clinical testing Variant summary: STXBP2 c.1393C>T (p.Arg465Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 241660 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in STXBP2 causing Familial Hemophagocytic Lymphohistiocytosis (0.00012 vs 0.0022), allowing no conclusion about variant significance. c.1393C>T has been reported in the literature in an individual affected with Familial Hemophagocytic Lymphohistiocytosis (Miao_2019). This report does not provide unequivocal conclusions about association of the variant with Familial Hemophagocytic Lymphohistiocytosis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 30899265). ClinVar contains an entry for this variant (Variation ID: 538149). Based on the evidence outlined above, the variant was classified as uncertain significance.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV004526731 SCV005089929 uncertain significance not specified 2025-03-04 criteria provided, single submitter clinical testing

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