ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.10549A>G (p.Lys3517Glu)

gnomAD frequency: 0.00007  dbSNP: rs143187571
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000192802 SCV000249394 uncertain significance not specified 2014-10-09 criteria provided, single submitter clinical testing
GeneDx RCV000766563 SCV000577343 uncertain significance not provided 2022-08-12 criteria provided, single submitter clinical testing 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
Labcorp Genetics (formerly Invitae), Labcorp RCV001055358 SCV001219746 uncertain significance Cohen syndrome 2025-01-31 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 3542 of the VPS13B protein (p.Lys3542Glu). This variant is present in population databases (rs143187571, gnomAD 0.02%). 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: 212568). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt VPS13B protein function with a positive predictive value of 80%. 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.
Breakthrough Genomics, Breakthrough Genomics RCV000766563 SCV005196067 uncertain significance not provided criteria provided, single submitter not provided
Natera, Inc. RCV001055358 SCV001461457 uncertain significance Cohen syndrome 2020-01-24 no assertion criteria provided clinical testing

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