ClinVar Miner

Submissions for variant NM_052989.3(IFT122):c.3265+1G>A

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV004725920 SCV005333915 pathogenic not provided 2024-03-22 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.; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV005023661 SCV005661417 likely pathogenic Cranioectodermal dysplasia 1 2024-03-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV005023661 SCV005755972 likely pathogenic Cranioectodermal dysplasia 1 2024-06-19 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 27 of the IFT122 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 IFT122 are known to be pathogenic (PMID: 20493458, 23826986, 26792575). This variant is present in population databases (rs767312059, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with IFT122-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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