ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.4676G>T (p.Gly1559Val)

gnomAD frequency: 0.00003  dbSNP: rs578203757
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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 RCV001038233 SCV001201696 uncertain significance Cohen syndrome 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1584 of the VPS13B protein (p.Gly1584Val). This variant is present in population databases (rs578203757, gnomAD 0.003%). 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: 836994). 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 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.
New York Genome Center RCV001038233 SCV002764419 uncertain significance Cohen syndrome 2021-10-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV004031067 SCV004978151 uncertain significance Inborn genetic diseases 2023-11-28 criteria provided, single submitter clinical testing The c.4751G>T (p.G1584V) alteration is located in exon 30 (coding exon 29) of the VPS13B gene. This alteration results from a G to T substitution at nucleotide position 4751, causing the glycine (G) at amino acid position 1584 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001038233 SCV001456854 uncertain significance Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004743256 SCV005358797 uncertain significance VPS13B-related disorder 2024-03-19 no assertion criteria provided clinical testing The VPS13B c.4676G>T variant is predicted to result in the amino acid substitution p.Gly1559Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0029% 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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