ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.515_517del (p.Thr172del) (rs386833947)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049922 SCV000221070 likely pathogenic Finnish congenital nephrotic syndrome 2015-01-22 criteria provided, single submitter literature only
Institute of Human Genetics,Klinikum rechts der Isar RCV000049922 SCV000680319 likely pathogenic Finnish congenital nephrotic syndrome 2017-12-07 criteria provided, single submitter clinical testing
Mendelics RCV000049922 SCV001141052 pathogenic Finnish congenital nephrotic syndrome 2019-05-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000049922 SCV001362147 pathogenic Finnish congenital nephrotic syndrome 2019-09-19 criteria provided, single submitter clinical testing Variant summary: NPHS1 c.515_517delCCA (p.Thr172del) results in an in-frame deletion that is predicted to remove a threonine residue from the second immunoglobulin-like domain (IPR013162) of the encoded protein. The variant allele was found at a frequency of 8e-06 in 251116 control chromosomes (gnomAD). c.515_517delCCA has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with Nephrotic Syndrome, Type 1 (e.g. Buscher_2010, Machuca_2010). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Both laboratories classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049922 SCV000082331 probable-pathogenic Finnish congenital nephrotic syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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