ClinVar Miner

Submissions for variant NM_001163435.3(TBCK):c.2060-2A>G

gnomAD frequency: 0.00005  dbSNP: rs62321379
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
TIDEX, University of British Columbia RCV000210871 SCV000586847 likely pathogenic Hypotonia, infantile, with psychomotor retardation and characteristic facies 3 criteria provided, single submitter research
Invitae RCV001853381 SCV002228033 pathogenic not provided 2023-11-11 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 22 of the TBCK gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TBCK are known to be pathogenic (PMID: 27040692, 30103036). This variant is present in population databases (rs62321379, gnomAD 0.005%). Disruption of this splice site has been observed in individual(s) with TBCK-related conditions (PMID: 27040691, 30542205). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 225239). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001853381 SCV002552600 pathogenic not provided 2022-07-22 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 30542205, 27040691)
OMIM RCV000210871 SCV000267186 pathogenic Hypotonia, infantile, with psychomotor retardation and characteristic facies 3 2016-05-19 no assertion criteria provided literature only
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals RCV000210871 SCV000599271 likely pathogenic Hypotonia, infantile, with psychomotor retardation and characteristic facies 3 2016-06-20 no assertion criteria provided clinical testing

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