ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.5011C>T (p.Arg1671Ter)

gnomAD frequency: 0.00001  dbSNP: rs386834093
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523583 SCV000617296 pathogenic not provided 2023-06-14 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 29758347, 20921020, 31736247, 31618753, 36073289)
Labcorp Genetics (formerly Invitae), Labcorp RCV000050204 SCV001214723 pathogenic Cohen syndrome 2023-10-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1696*) 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 (rs386834093, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with Cohen syndrome (PMID: 20921020, 29758347). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56803). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV001267010 SCV001445191 pathogenic Inborn genetic diseases 2018-02-27 criteria provided, single submitter clinical testing
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000050204 SCV004804980 pathogenic Cohen syndrome 2024-03-17 criteria provided, single submitter research
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000050204 SCV000082780 probable-pathogenic Cohen syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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