ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.3027C>G (p.Tyr1009Ter) (rs762184939)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000668878 SCV000793551 pathogenic Finnish congenital nephrotic syndrome 2017-08-18 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000668878 SCV001372391 pathogenic Finnish congenital nephrotic syndrome 2020-06-25 criteria provided, single submitter clinical testing Variant summary: NPHS1 c.3027C>G (p.Tyr1009X) 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 8e-06 in 251488 control chromosomes. c.3027C>G has been reported in the literature in individuals affected with Nephrotic Syndrome, Type 1 and subsequently cited by others (example, Lee_2011, Wang_2017, Chen_2019, Abid_2018). 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 classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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