ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.7623T>A (p.Ser2541Arg)

gnomAD frequency: 0.00006  dbSNP: rs754632431
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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 RCV002045345 SCV002293031 uncertain significance Cohen syndrome 2022-03-10 criteria provided, single submitter clinical testing This sequence change replaces serine with arginine at codon 2566 of the VPS13B protein (p.Ser2566Arg). The serine residue is weakly conserved and there is a moderate physicochemical difference between serine and arginine. This variant is present in population databases (rs754632431, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with VPS13B-related conditions. 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.
Ambry Genetics RCV002398091 SCV002673195 uncertain significance Inborn genetic diseases 2019-08-08 criteria provided, single submitter clinical testing The p.S2566R variant (also known as c.7698T>A), located in coding exon 41 of the VPS13B gene, results from a T to A substitution at nucleotide position 7698. The serine at codon 2566 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004744205 SCV005358355 uncertain significance VPS13B-related disorder 2024-04-09 no assertion criteria provided clinical testing The VPS13B c.7623T>A variant is predicted to result in the amino acid substitution p.Ser2541Arg. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.032% of alleles in individuals of African 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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