ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.903_906del (p.Leu302fs) (rs1595763662)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001009109 SCV001168920 likely pathogenic not provided 2019-10-28 criteria provided, single submitter clinical testing Frameshift variant in the C-terminus predicted to result in protein truncation, as the last 143 amino acids are lost and replaced with 15 incorrect amino acids (Stenson et al., 2014); Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016)
Invitae RCV001235430 SCV001408115 pathogenic Legius syndrome 2019-11-07 criteria provided, single submitter clinical testing This sequence change results in a premature translational stop signal in the SPRED1 gene (p.Leu302Valfs*16). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 143 amino acids of the SPRED1 protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SPRED1-related conditions. This variant disrupts the C-terminus of the SPRED1 protein. Other variant(s) that disrupt this region (p.Arg325*) have been determined to be pathogenic (PMID: 17704776, 25883013). 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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