ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.1590G>A (p.Met530Ile)

gnomAD frequency: 0.00006  dbSNP: rs200519753
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000808268 SCV000948368 uncertain significance Cohen syndrome 2022-07-30 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 530 of the VPS13B protein (p.Met530Ile). This variant is present in population databases (rs200519753, gnomAD 0.01%). 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: 652672). 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: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). 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.
GeneDx RCV001577950 SCV001805449 uncertain significance not provided 2021-09-07 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Natera, Inc. RCV000808268 SCV001454807 uncertain significance Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing
GenomeConnect - Invitae Patient Insights Network RCV000808268 SCV001749690 not provided Cohen syndrome no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 10-09-2018 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
PreventionGenetics, part of Exact Sciences RCV003411785 SCV004116043 uncertain significance VPS13B-related disorder 2024-08-19 no assertion criteria provided clinical testing The VPS13B c.1590G>A variant is predicted to result in the amino acid substitution p.Met530Ile. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.013% of alleles in individuals of European (Non-Finnish) 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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