ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.6262G>A (p.Asp2088Asn)

gnomAD frequency: 0.00001  dbSNP: rs1056435586
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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 RCV001239379 SCV001412252 uncertain significance Cohen syndrome 2022-05-08 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 2113 of the VPS13B protein (p.Asp2113Asn). This variant is present in population databases (no rsID available, gnomAD 0.05%). 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: 965028). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). 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.
Genome-Nilou Lab RCV001239379 SCV001806350 uncertain significance Cohen syndrome 2021-07-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV002563940 SCV003680215 uncertain significance Inborn genetic diseases 2022-08-03 criteria provided, single submitter clinical testing The c.6337G>A (p.D2113N) alteration is located in exon 36 (coding exon 35) of the VPS13B gene. This alteration results from a G to A substitution at nucleotide position 6337, causing the aspartic acid (D) at amino acid position 2113 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV003127716 SCV003803257 uncertain significance not provided 2022-08-08 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Identified in trans with another VPS13B variant in an individual with atrioventricular septal heart defect, but additional phenotypic information was not included and the individual harbored several variants in other genes (Priest et al., 2016); This variant is associated with the following publications: (PMID: 27058611)
Natera, Inc. RCV001239379 SCV002082606 uncertain significance Cohen syndrome 2020-04-16 no assertion criteria provided clinical testing

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