ClinVar Miner

Submissions for variant NM_004646.4(NPHS1):c.2071+2T>C

dbSNP: rs386833901
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049873 SCV000792043 likely pathogenic Finnish congenital nephrotic syndrome 2017-06-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001376868 SCV001574054 pathogenic not provided 2023-09-20 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 15 of the NPHS1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NPHS1 are known to be pathogenic (PMID: 11317351, 11854170, 12039988). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with clinical features of nephrotic syndrome (PMID: 11317351, 20507940, 34859019). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56460). For these reasons, this variant has been classified as Pathogenic.
Vasylyeva lab, Texas Tech University Health Sciences Center RCV003407432 SCV004123137 likely pathogenic Infantile Nephrotic syndrome 2022-09-26 criteria provided, single submitter clinical testing
Baylor Genetics RCV000049873 SCV004191386 pathogenic Finnish congenital nephrotic syndrome 2023-10-17 criteria provided, single submitter clinical testing
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049873 SCV000082282 probable-pathogenic Finnish congenital nephrotic syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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