ClinVar Miner

Submissions for variant NM_020461.4(TUBGCP6):c.589T>C (p.Ser197Pro)

gnomAD frequency: 0.00113  dbSNP: rs138586345
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000997946 SCV001153722 likely benign not provided 2023-02-01 criteria provided, single submitter clinical testing TUBGCP6: BP4
Invitae RCV000997946 SCV001232598 uncertain significance not provided 2022-10-04 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 197 of the TUBGCP6 protein (p.Ser197Pro). This variant is present in population databases (rs138586345, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with TUBGCP6-related conditions. ClinVar contains an entry for this variant (Variation ID: 809385). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV000997946 SCV001824027 uncertain significance not provided 2022-05-24 criteria provided, single submitter clinical testing Observed with a nonsense variant on the opposite allele (in trans) in a patient with lissencephaly, generalized tonic clonic seizures, myoclonic seizures, and moderate intellectual disability in the published literature (Kolbjer et al., 2021); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 33453472, 33726816)
Revvity Omics, Revvity Omics RCV001535501 SCV003819881 uncertain significance Microcephaly and chorioretinopathy 1 2023-07-31 criteria provided, single submitter clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV003493768 SCV004242513 uncertain significance not specified 2024-02-06 criteria provided, single submitter clinical testing
GenomeConnect - Invitae Patient Insights Network RCV001535501 SCV001749454 not provided Microcephaly and chorioretinopathy 1 no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 11-05-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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