ClinVar Miner

Submissions for variant NM_001077350.3(NPRL3):c.377del (p.Val126fs) (rs1596526915)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001008518 SCV001168290 likely pathogenic not provided 2019-01-08 criteria provided, single submitter clinical testing A variant that is likely pathogenic has been identified in the NPRL3 gene. The c.377delT variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.377delT variant in the NPRL3 gene causes a frameshift starting with codon Valine 126, changes this amino acid to a Glycine residue and creates a premature Stop codon at position 5 of the new reading frame, denoted p.Val126GlyfsX5. This frameshift variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.377delT variant is not observed in large population cohorts (Lek et al., 2016). Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.
Invitae RCV001067357 SCV001232414 pathogenic Epilepsy, familial focal, with variable foci 3 2019-05-10 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Val126Glyfs*5) in the NPRL3 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with NPRL3-related conditions. Loss-of-function variants in NPRL3 are known to be pathogenic (PMID: 26285051, 26505888). For these reasons, this variant has been classified as Pathogenic.

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