ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.313G>A (p.Asp105Asn) (rs386833932)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049906 SCV000793653 likely pathogenic Finnish congenital nephrotic syndrome 2017-08-22 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000049906 SCV000919900 likely pathogenic Finnish congenital nephrotic syndrome 2018-11-02 criteria provided, single submitter clinical testing Variant summary: NPHS1 c.313G>A (p.Asp105Asn) results in a conservative amino acid change located in the Immunoglobulin-like domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.6e-06 in 275106 control chromosomes (gnomAD and publications). The variant, c.313G>A, has been reported in the literature in individuals affected with Nephrotic Syndrome, Type 1 (Sadowski_2014, Sako_2005, Sen_2017). 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 classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049906 SCV000082315 probable-pathogenic Finnish congenital nephrotic syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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