ClinVar Miner

Submissions for variant NM_006949.4(STXBP2):c.533C>T (p.Thr178Met)

gnomAD frequency: 0.00003  dbSNP: rs762234445
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001243664 SCV001416837 uncertain significance Familial hemophagocytic lymphohistiocytosis 5 2022-09-01 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 178 of the STXBP2 protein (p.Thr178Met). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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: 968511). 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: "Deleterious"; 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.
Baylor Genetics RCV001243664 SCV001521987 uncertain significance Familial hemophagocytic lymphohistiocytosis 5 2020-08-03 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Ambry Genetics RCV003284114 SCV003956338 uncertain significance Inborn genetic diseases 2023-05-03 criteria provided, single submitter clinical testing The c.533C>T (p.T178M) alteration is located in exon 7 (coding exon 7) of the STXBP2 gene. This alteration results from a C to T substitution at nucleotide position 533, causing the threonine (T) at amino acid position 178 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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