ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.10687G>A (p.Gly3563Arg) (rs150767461)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000719607 SCV000850476 uncertain significance History of neurodevelopmental disorder 2017-02-22 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient evidence
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000723856 SCV000203797 uncertain significance not provided 2014-02-28 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000765983 SCV000897413 uncertain significance Cohen syndrome 2018-10-31 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000154133 SCV000597899 uncertain significance not specified 2017-01-12 criteria provided, single submitter clinical testing
Invitae RCV000765983 SCV000937858 uncertain significance Cohen syndrome 2018-11-29 criteria provided, single submitter clinical testing This sequence change replaces glycine with arginine at codon 3563 of the VPS13B protein (p.Gly3563Arg). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and arginine. This variant is present in population databases (rs150767461, ExAC 0.07%). This variant has not been reported in the literature in individuals with VPS13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 167836). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0". The arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.

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