ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6190A>G (p.Met2064Val)

gnomAD frequency: 0.00001  dbSNP: rs200554315
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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 RCV001373295 SCV001570003 uncertain significance Cohen syndrome 2022-08-03 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2089 of the VPS13B protein (p.Met2089Val). This variant is present in population databases (rs200554315, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1063458). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV004037563 SCV004978158 uncertain significance Inborn genetic diseases 2024-02-12 criteria provided, single submitter clinical testing The c.6265A>G (p.M2089V) alteration is located in exon 36 (coding exon 35) of the VPS13B gene. This alteration results from a A to G substitution at nucleotide position 6265, causing the methionine (M) at amino acid position 2089 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001373295 SCV002082602 uncertain significance Cohen syndrome 2020-09-24 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004743440 SCV005357077 uncertain significance VPS13B-related disorder 2024-08-30 no assertion criteria provided clinical testing The VPS13B c.6190A>G variant is predicted to result in the amino acid substitution p.Met2064Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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