ClinVar Miner

Submissions for variant NM_000112.4(SLC26A2):c.1655C>A (p.Ser552Ter)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193470 SCV001362331 likely pathogenic Osteochondrodysplasia 2019-05-10 criteria provided, single submitter clinical testing Variant summary: SLC26A2 c.1655C>A (p.Ser552X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. A truncation downstream of this position (c.1724delA (p.Lys575fsX10)) has been classified as pathogenic by our laboratory. The variant was absent in 250928 control chromosomes (gnomAD). To our knowledge, no occurrence of c.1655C>A in individuals affected with Sulfate Transporter-Related Osteochondrodysplasia and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae RCV001390701 SCV001592502 pathogenic Achondrogenesis, type IB; Atelosteogenesis type II; Multiple epiphyseal dysplasia type 4; Diastrophic dysplasia 2020-06-30 criteria provided, single submitter clinical testing This sequence change results in a premature translational stop signal in the SLC26A2 gene (p.Ser552*). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 188 amino acids of the SLC26A2 protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SLC26A2-related conditions. This variant disrupts the C-terminus of the SLC26A2 protein. Other variant(s) that disrupt this region (p.Thr689Serfs*22) have been determined to be pathogenic (Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. For these reasons, this variant has been classified as Pathogenic.

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