ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.7753G>A (p.Glu2585Lys) (rs111751379)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000081914 SCV000113849 benign not specified 2012-10-11 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000081914 SCV000249420 likely benign not specified 2016-12-09 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000081914 SCV000316202 likely benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000081914 SCV000512679 likely benign not specified 2016-05-11 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000513903 SCV000611049 likely benign not provided 2017-03-17 criteria provided, single submitter clinical testing
Invitae RCV000547888 SCV000630887 benign Cohen syndrome 2020-12-08 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000513903 SCV000841644 likely benign not provided 2017-12-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV000717784 SCV000848643 likely benign History of neurodevelopmental disorder 2019-05-06 criteria provided, single submitter clinical testing In silico models in agreement (benign) ;Sub-population frequency in support of benign classification (not ava blue, manual h-w)
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000547888 SCV000899085 uncertain significance Cohen syndrome 2017-12-12 criteria provided, single submitter clinical testing VPS13B NM_017890.4 exon 42 p.Glu2585Lys (c.7753G>A): This variant has not been reported in the literature but is present in 0.5% (646/126280) of European alleles, including 3 homozygotes in the Genome Aggregation Database ( This variant is present in ClinVar, with several labs classifying this variant as likely benign or benign (Variation ID:95867). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Molecular Genetics Laboratory,Institute for Ophthalmic Research RCV001199598 SCV001162769 pathogenic Retinitis pigmentosa 2020-01-09 criteria provided, single submitter research
Illumina Clinical Services Laboratory,Illumina RCV000547888 SCV001324016 likely benign Cohen syndrome 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Nilou-Genome Lab RCV000547888 SCV001653379 likely benign Cohen syndrome 2021-05-18 criteria provided, single submitter clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000513903 SCV001798786 likely benign not provided no assertion criteria provided clinical testing

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