ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.8983C>T (p.Pro2995Ser)

dbSNP: rs1180231209
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001319041 SCV001509767 uncertain significance Cohen syndrome 2022-07-06 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 3020 of the VPS13B protein (p.Pro3020Ser). This variant is not present in population databases (gnomAD no frequency). 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: 1019585). 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004699305 SCV005202827 uncertain significance not specified 2024-07-24 criteria provided, single submitter clinical testing Variant summary: VPS13B c.9058C>T (p.Pro3020Ser) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250184 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.9058C>T in individuals affected with Cohen Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1019585). Based on the evidence outlined above, the variant was classified as uncertain significance.
Natera, Inc. RCV001319041 SCV002082694 uncertain significance Cohen syndrome 2021-05-11 no assertion criteria provided clinical testing

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