ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.8776AAG[1] (p.Lys2927del)

dbSNP: rs549810522
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000286330 SCV000336249 uncertain significance not provided 2015-10-19 criteria provided, single submitter clinical testing
Counsyl RCV000671822 SCV000796845 uncertain significance Cohen syndrome 2018-01-02 criteria provided, single submitter clinical testing
Invitae RCV000671822 SCV001224796 uncertain significance Cohen syndrome 2022-10-18 criteria provided, single submitter clinical testing This variant, c.8854_8856del, results in the deletion of 1 amino acid(s) of the VPS13B protein (p.Lys2952del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs549810522, gnomAD 0.09%), including at least one homozygous and/or hemizygous individual. 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: 283889). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.
GeneDx RCV000286330 SCV001780675 uncertain significance not provided 2021-07-27 criteria provided, single submitter clinical testing In-frame deletion of one amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV000671822 SCV003820444 uncertain significance Cohen syndrome 2022-05-12 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003409408 SCV004109466 uncertain significance VPS13B-related disorder 2023-09-14 criteria provided, single submitter clinical testing The VPS13B c.8779_8781delAAG variant is predicted to result in an in-frame deletion (p.Lys2927del). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.092% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/8-100831793-TAAG-T)AG-T), which is likely too common for an undocumented disease-causing variant. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Natera, Inc. RCV000671822 SCV001461445 benign Cohen syndrome 2020-04-16 no assertion criteria provided clinical testing

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