ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.1701C>A (p.Cys567Ter) (rs386833887)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049858 SCV000220423 likely pathogenic Finnish congenital nephrotic syndrome 2014-06-18 criteria provided, single submitter literature only
Athena Diagnostics Inc RCV000992445 SCV001144760 pathogenic not provided 2019-02-22 criteria provided, single submitter clinical testing The variant creates a premature nonsense codon, and is therefore predicted to result in the loss of a functional protein. Found in at least one symptomatic patient, and found in general population data that is consistent with pathogenicity. Occurs in three or more cases with a recessive pathogenic variant in the same gene.
Baylor Genetics RCV000049858 SCV001163805 pathogenic Finnish congenital nephrotic syndrome criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000049858 SCV001370696 pathogenic Finnish congenital nephrotic syndrome 2020-05-04 criteria provided, single submitter clinical testing Variant summary: NPHS1 c.1701C>A (p.Cys567X) 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. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 3.2e-05 in 250782 control chromosomes. c.1701C>A has been reported in the literature in individuals affected with Nephrotic Syndrome, Type 1 (examples- Beltcheva_2001, Santin_2009, Ovunc_2012). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and cited the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049858 SCV000082267 probable-pathogenic Finnish congenital nephrotic syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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