ClinVar Miner

Submissions for variant NM_001011658.4(TRAPPC2):c.239-10_239-7del

dbSNP: rs2146773091
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India RCV001806356 SCV002053887 pathogenic Spondyloepiphyseal dysplasia tarda, X-linked criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001869566 SCV002270557 uncertain significance not provided 2023-11-02 criteria provided, single submitter clinical testing This sequence change falls in intron 4 of the TRAPPC2 gene. It does not directly change the encoded amino acid sequence of the TRAPPC2 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with clinical features of spondyloepiphyseal dysplasia tarda (PMID: 11349230; Invitae). This variant is also known as IVS4-9—12del. ClinVar contains an entry for this variant (Variation ID: 1332782). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.
PreventionGenetics, part of Exact Sciences RCV003401727 SCV004103978 likely pathogenic TRAPPC2-related disorder 2024-01-25 no assertion criteria provided clinical testing The TRAPPC2 c.239-10_239-7delATTA variant is predicted to result in an intronic deletion. This variant was reported in an individual with spondyloepiphyseal dysplasia tarda (reported as as IVS4-9-12del, Gedeon et al. 2001. PubMed ID: 11349230). Similar nearby intronic deletions were reported in individuals with spondyloepiphyseal dysplasia tarda (inherited from the unaffected mother, reported as c.341-(11_9) in Davis. 2014. PubMed ID: 23656395; reported as as IVS4-4-11del in Gedeon et al. 2001. PubMed ID: 11349230).  This variant has not been reported in a large population database, indicating this variant is rare. The variant has been reported to segregate with skeletal dysplasia in a family (Internal Data, PreventionGenetics). This variant is interpreted as Likely Pathogenic.

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