ClinVar Miner

Submissions for variant NM_014625.4(NPHS2):c.104dup (p.Arg36fs)

dbSNP: rs1320543506
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000516610 SCV000614343 pathogenic not provided 2014-09-11 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000005693 SCV001983641 pathogenic Nephrotic syndrome, type 2 2021-09-12 criteria provided, single submitter clinical testing Variant summary: NPHS2 c.104dupG (p.Arg36ProfsX34) 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 90220 control chromosomes. c.104dupG has been reported in the literature in individuals affected with Nephrotic Syndrome, Type 2 (example, Boute_2000, Machuca_2010, Giglio_2015). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Genome-Nilou Lab RCV000005693 SCV004049303 pathogenic Nephrotic syndrome, type 2 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV000005693 SCV004191538 pathogenic Nephrotic syndrome, type 2 2023-11-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000516610 SCV004293852 pathogenic not provided 2023-10-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg36Profs*34) in the NPHS2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHS2 are known to be pathogenic (PMID: 10742096, 14701729, 15253708, 23595123). This variant is present in population databases (no rsID available, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with nephrotic syndrome (PMID: 10742096). ClinVar contains an entry for this variant (Variation ID: 447876). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000005693 SCV000025875 pathogenic Nephrotic syndrome, type 2 2000-04-01 no assertion criteria provided literature only

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