ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.1915C>T (p.Arg639Ter) (rs764776104)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000255734 SCV000322116 pathogenic not provided 2018-11-30 criteria provided, single submitter clinical testing The R639X pathogenic variant in the VPS13B gene has been reported previously in a patient with Cohen syndrome including features of microcephaly, short stature, and truncal obesity. This individual was presumed compound heterozygous for this pathogenic variant and another protein truncating/loss-of-function variant; this patient also harbored a pathogenic variant in the ELANE gene, which was felt to be related to her severe neutropenia (Beene et al., 2015). The R639X variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R639X variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret R639X as a pathogenic variant.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000255734 SCV000703985 pathogenic not provided 2016-12-12 criteria provided, single submitter clinical testing
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000824874 SCV000965781 likely pathogenic Cohen syndrome 2016-01-04 criteria provided, single submitter clinical testing
Counsyl RCV000824874 SCV001132510 likely pathogenic Cohen syndrome 2015-08-20 no assertion criteria provided clinical testing
Natera, Inc. RCV000824874 SCV001454810 pathogenic Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing

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