ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.8390A>G (p.Tyr2797Cys)

gnomAD frequency: 0.00004  dbSNP: rs371325199
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000634099 SCV000755377 uncertain significance Cohen syndrome 2022-10-12 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 2822 of the VPS13B protein (p.Tyr2822Cys). This variant is present in population databases (rs371325199, gnomAD 0.01%). This missense change has been observed in individual(s) with Cohen syndrome (PMID: 16648375). ClinVar contains an entry for this variant (Variation ID: 528842). 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.
Ambry Genetics RCV002529820 SCV003719418 uncertain significance Inborn genetic diseases 2022-02-26 criteria provided, single submitter clinical testing The c.8465A>G (p.Y2822C) alteration is located in exon 46 (coding exon 45) of the VPS13B gene. This alteration results from a A to G substitution at nucleotide position 8465, causing the tyrosine (Y) at amino acid position 2822 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Mayo Clinic Laboratories, Mayo Clinic RCV004791649 SCV005409500 uncertain significance not provided 2023-12-06 criteria provided, single submitter clinical testing BP1
Natera, Inc. RCV000634099 SCV001460982 uncertain significance Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003905701 SCV004722377 uncertain significance VPS13B-related disorder 2024-02-27 no assertion criteria provided clinical testing The VPS13B c.8390A>G variant is predicted to result in the amino acid substitution p.Tyr2797Cys. This variant has been reported in an individual with Cohen syndrome, but no additional studies were performed to help assess its pathogenicity (Seifert et al 2006. PubMed ID: 16648375). This variant is reported in 0.011% 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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