ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.4396G>T (p.Glu1466Ter)

gnomAD frequency: 0.00004  dbSNP: rs120074151
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000002956 SCV000699447 pathogenic Cohen syndrome 2017-06-22 criteria provided, single submitter clinical testing Variant summary: The VPS13B c.4471G>T (p.Glu1491X) variant results in a premature termination codon, predicted to cause a truncated or absent VPS13B protein due to nonsense mediated decay, which are commonly known mechanisms for disease. One in silico tool predicts a damaging outcome for this variant. This variant is absent in 121380 control chromosomes. The variant has been reported homozygously in multiple affected individuals and was shown to segregate with the disease in at least two Cohen families. Taken together, this variant is classified as pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000002956 SCV000893770 pathogenic Cohen syndrome 2018-10-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000002956 SCV001381909 pathogenic Cohen syndrome 2023-10-04 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu1491*) in the VPS13B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in VPS13B are known to be pathogenic (PMID: 15141358, 16648375, 20461111). This variant is present in population databases (rs120074151, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with Cohen syndrome (PMID: 15141358). ClinVar contains an entry for this variant (Variation ID: 2822). For these reasons, this variant has been classified as Pathogenic.
Genetics and Molecular Pathology, SA Pathology RCV000002956 SCV004175480 pathogenic Cohen syndrome 2023-04-26 criteria provided, single submitter clinical testing
OMIM RCV000002956 SCV000023114 pathogenic Cohen syndrome 2004-07-01 no assertion criteria provided literature only
Counsyl RCV000002956 SCV001132506 likely pathogenic Cohen syndrome 2015-03-03 no assertion criteria provided clinical testing
Natera, Inc. RCV000002956 SCV001456852 pathogenic Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing

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