ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.10663G>A (p.Val3555Met)

gnomAD frequency: 0.00002  dbSNP: rs745866775
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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 RCV000193835 SCV000249395 uncertain significance not specified 2014-12-17 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001060335 SCV001225015 uncertain significance Cohen syndrome 2022-02-08 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 3580 of the VPS13B protein (p.Val3580Met). This variant is present in population databases (rs745866775, gnomAD 0.03%). 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: 212569). 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: "Possibly Damaging"; 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.
Ambry Genetics RCV003372646 SCV004061950 uncertain significance Inborn genetic diseases 2023-06-26 criteria provided, single submitter clinical testing The c.10738G>A (p.V3580M) alteration is located in exon 56 (coding exon 55) of the VPS13B gene. This alteration results from a G to A substitution at nucleotide position 10738, causing the valine (V) at amino acid position 3580 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001060335 SCV002082753 uncertain significance Cohen syndrome 2019-11-11 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004742325 SCV005348222 uncertain significance VPS13B-related disorder 2024-05-07 no assertion criteria provided clinical testing The VPS13B c.10663G>A variant is predicted to result in the amino acid substitution p.Val3555Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.029% of alleles in individuals of Latino 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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