ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.565G>T (p.Glu189Ter) (rs139598219)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169154 SCV000220381 likely pathogenic Finnish congenital nephrotic syndrome 2014-06-06 criteria provided, single submitter literature only
Athena Diagnostics Inc RCV000712433 SCV000842926 pathogenic not provided 2016-05-20 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000169154 SCV001370676 pathogenic Finnish congenital nephrotic syndrome 2020-05-17 criteria provided, single submitter clinical testing Variant summary: NPHS1 c.565G>T (p.Glu189X) 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 was absent in 251490 control chromosomes. c.565G>T has been reported in the literature in at-least one individual affected with Nephrotic Syndrome, Type 1 (example, Chaudhuri_2012) and has also been cited elsewhere (example, Holmberg_2014). 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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