ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.728_729del (p.Pro243fs) (rs1599845714)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000992447 SCV001144764 likely pathogenic not provided 2019-02-25 criteria provided, single submitter clinical testing The variant results in a shift of the reading frame, and is therefore predicted to result in the loss of a functional protein.
Integrated Genetics/Laboratory Corporation of America RCV001255501 SCV001431931 likely pathogenic Finnish congenital nephrotic syndrome 2020-08-03 criteria provided, single submitter clinical testing Variant summary: NPHS1 c.728_729delCT (p.Pro243ArgfsX9) 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 248410 control chromosomes (gnomAD). To our knowledge, no occurrence of c.728_729delCT in individuals affected with Nephrotic Syndrome, Type 1 and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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