ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.3866C>G (p.Thr1289Ser)

gnomAD frequency: 0.00178  dbSNP: rs145569846
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000081898 SCV000113833 uncertain significance not provided 2013-10-04 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000530711 SCV000630874 likely benign Cohen syndrome 2024-01-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002311681 SCV000847118 likely benign Inborn genetic diseases 2018-09-26 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000530711 SCV000899082 uncertain significance Cohen syndrome 2021-09-17 criteria provided, single submitter clinical testing VPS13B NM_017890.4 exon 25 p.Thr1289Ser (c.3866C>G): This variant has been reported in the literature as a compound heterozygote (in trans with a multi-exon deletion of this gene) in 1 individual with a diagnosis of Cohen syndrome (Rivera-Brugues 2011 PMID:20921020, gene identified as alternate name COH1). However, this variant is present in 0.5% (125/24018) of African alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs145569846). This variant is present in ClinVar (Variation ID:95851). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Mendelics RCV000530711 SCV001137683 benign Cohen syndrome 2023-08-22 criteria provided, single submitter clinical testing
GeneDx RCV000081898 SCV001779477 likely benign not provided 2020-10-14 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 20921020)
Revvity Omics, Revvity RCV000530711 SCV003820434 uncertain significance Cohen syndrome 2019-08-06 criteria provided, single submitter clinical testing
Natera, Inc. RCV000530711 SCV001456848 likely benign Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000081898 SCV001958134 uncertain significance not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000081898 SCV001975329 uncertain significance not provided no assertion criteria provided clinical testing

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