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 2018-11-01 criteria provided, single submitter clinical testing The c.903_906delGTTA variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is not observed in large population cohorts (Lek et al., 2016). It causes a frameshift starting with codon Leucine 302, changes this amino acid to a Valine residue and creates a premature Stop codon at position 16 of the new reading frame, denoted p.Leu302ValfsX16. This variant is predicted to cause loss of normal protein function through protein truncation. We interpret this variant as likely pathogenic.
Invitae RCV001235430 SCV001408115 pathogenic Legius syndrome 2019-11-20 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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