ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.2470T>G (p.Ser824Ala)

gnomAD frequency: 0.00012  dbSNP: rs149866274
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000175216 SCV000226661 uncertain significance not provided 2014-06-24 criteria provided, single submitter clinical testing
Invitae RCV001082387 SCV001091402 likely benign Cohen syndrome 2024-01-29 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000175216 SCV001245917 uncertain significance not provided 2019-08-01 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001082387 SCV001325569 uncertain significance Cohen syndrome 2017-09-19 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Ambry Genetics RCV002516667 SCV003682603 uncertain significance Inborn genetic diseases 2022-02-28 criteria provided, single submitter clinical testing The c.2470T>G (p.S824A) alteration is located in exon 17 (coding exon 16) of the VPS13B gene. This alteration results from a T to G substitution at nucleotide position 2470, causing the serine (S) at amino acid position 824 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV003416074 SCV004107014 uncertain significance VPS13B-related disorder 2023-12-08 criteria provided, single submitter clinical testing The VPS13B c.2470T>G variant is predicted to result in the amino acid substitution p.Ser824Ala. This variant has been reported in the homozygous state in one individual with features of Cohen syndrome (Yu et al. 2013. PubMed ID: 23352163). However, pathogenicity was not clearly established in this study. In a functional study, the VPS13B protein with the p.Ser824Ala substitution behaved similarly to wild-type (Zorn et al. 2022. PubMed ID: 35690661). This variant is reported in 0.031% of alleles in individuals of European (Non-Finnish) descent in gnomAD, including one homozygous individual. Although we suspect that this variant may be benign, at this time, its clinical significance is uncertain due to the absence of conclusive functional and genetic evidence.
Natera, Inc. RCV001082387 SCV002079513 likely benign Cohen syndrome 2021-10-12 no assertion criteria provided clinical testing

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