ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6698T>C (p.Leu2233Pro)

gnomAD frequency: 0.00001  dbSNP: rs776873589
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001229066 SCV001401498 uncertain significance Cohen syndrome 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 2258 of the VPS13B protein (p.Leu2258Pro). This variant is present in population databases (rs776873589, 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: 956291). 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.
PreventionGenetics, part of Exact Sciences RCV003898217 SCV004713658 likely pathogenic VPS13B-related disorder 2024-07-04 no assertion criteria provided clinical testing The VPS13B c.6698T>C variant is predicted to result in the amino acid substitution p.Leu2233Pro. To our knowledge, this variant has not been reported in the literature. At PreventionGenetics, we identified this variant in trans with a pathogenic splice site variant in an affected individual (internal data). This variant is reported in 0.0026% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as likely pathogenic.

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