ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.8825T>C (p.Met2942Thr)

gnomAD frequency: 0.00001  dbSNP: rs1305759367
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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 RCV001203383 SCV001374546 uncertain significance Cohen syndrome 2019-10-15 criteria provided, single submitter clinical testing This sequence change replaces methionine with threonine at codon 2967 of the VPS13B protein (p.Met2967Thr). The methionine residue is moderately conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with VPS13B-related conditions. 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: "Benign"; 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.
Ambry Genetics RCV003373024 SCV004092976 uncertain significance Inborn genetic diseases 2023-08-21 criteria provided, single submitter clinical testing The c.8900T>C (p.M2967T) alteration is located in exon 49 (coding exon 48) of the VPS13B gene. This alteration results from a T to C substitution at nucleotide position 8900, causing the methionine (M) at amino acid position 2967 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV003398926 SCV004121156 uncertain significance VPS13B-related disorder 2022-10-18 criteria provided, single submitter clinical testing The VPS13B c.8825T>C variant is predicted to result in the amino acid substitution p.Met2942Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0016% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/8-100832181-T-C). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Natera, Inc. RCV001203383 SCV002082690 uncertain significance Cohen syndrome 2020-03-10 no assertion criteria provided clinical testing

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