ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.2917A>G (p.Ser973Gly)

gnomAD frequency: 0.00006  dbSNP: rs749751670
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002313544 SCV000848609 uncertain significance Inborn genetic diseases 2024-06-17 criteria provided, single submitter clinical testing The c.2917A>G (p.S973G) alteration is located in exon 20 (coding exon 19) of the VPS13B gene. This alteration results from a A to G substitution at nucleotide position 2917, causing the serine (S) at amino acid position 973 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Pars Genome Lab RCV001526427 SCV001736812 uncertain significance Cohen syndrome 2021-05-18 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001526427 SCV001806191 uncertain significance Cohen syndrome 2021-07-22 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001526427 SCV002792188 uncertain significance Cohen syndrome 2021-07-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001526427 SCV003018961 uncertain significance Cohen syndrome 2022-09-28 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 973 of the VPS13B protein (p.Ser973Gly). This variant is present in population databases (rs749751670, gnomAD 0.02%). 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: 588603). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt VPS13B protein function. 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.
Natera, Inc. RCV001526427 SCV002079540 uncertain significance Cohen syndrome 2019-11-11 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003420277 SCV004113631 uncertain significance VPS13B-related disorder 2024-01-27 no assertion criteria provided clinical testing The VPS13B c.2917A>G variant is predicted to result in the amino acid substitution p.Ser973Gly. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.023% of alleles in individuals of Latino 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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