ClinVar Miner

Submissions for variant NM_014625.3(NPHS2):c.467dup (p.Leu156fs) (rs528833893)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000673011 SCV000798175 pathogenic Idiopathic nephrotic syndrome 2018-02-27 criteria provided, single submitter clinical testing
Genomic Research Center,Shahid Beheshti University of Medical Sciences RCV000673011 SCV000845598 uncertain significance Idiopathic nephrotic syndrome 2018-08-07 criteria provided, single submitter clinical testing
Department of Genetics,Sultan Qaboos University Hospital, Oman RCV000673011 SCV000891537 pathogenic Idiopathic nephrotic syndrome 2017-12-30 criteria provided, single submitter curation
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000673011 SCV000919902 pathogenic Idiopathic nephrotic syndrome 2017-09-11 criteria provided, single submitter clinical testing Variant summary: The NPHS2 c.467dupT (p.Leu156PhefsX11) variant results in a premature termination codon, predicted to cause a truncated or absent NPHS2 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. One in silico tool predicts a damaging outcome for this variant. This variant was found in 42/199282 control chromosomes at a frequency of 0.0002108, which does not exceed the estimated maximal expected allele frequency of a pathogenic NPHS2 variant (0.0017678). This variant has been reported in multiple patients with steroid-resistant nephrotic syndrome and classified as pathogenic by a reputable database. Taken together, this variant is classified as pathogenic.
Invitae RCV001069505 SCV001234675 pathogenic not provided 2020-08-22 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu156Phefs*11) in the NPHS2 gene. It is expected to result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has been observed in several individuals affected with steroid-resistant nephrotic syndrome or focal segmental glomerulosclerosis (PMID: 11729243, 25903641, 28204945, 19674119). ClinVar contains an entry for this variant (Variation ID: 556941). Loss-of-function variants in NPHS2 are known to be pathogenic (PMID: 10742096, 14701729, 15253708, 23595123). For these reasons, this variant has been classified as Pathogenic.
Institute of Human Genetics, Klinikum rechts der Isar RCV000673011 SCV001150183 pathogenic Idiopathic nephrotic syndrome 2019-05-08 no assertion criteria provided clinical testing
Natera, Inc. RCV001273619 SCV001456819 pathogenic Steroid-resistant nephrotic syndrome 2020-09-16 no assertion criteria provided clinical testing

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