ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.1889_1892del (p.Pro630fs)

gnomAD frequency: 0.00005  dbSNP: rs1368105372
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001244264 SCV001417472 pathogenic Nephronophthisis 2022-12-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 562366). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Pro630Argfs*69) in the NPHP4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHP4 are known to be pathogenic (PMID: 12205563, 23559409).
GeneDx RCV000681825 SCV001772172 likely pathogenic not provided 2020-04-17 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31589614)
Fulgent Genetics, Fulgent Genetics RCV002493130 SCV002780690 pathogenic Nephronophthisis 4; Senior-Loken syndrome 4 2022-03-24 criteria provided, single submitter clinical testing
Gharavi Laboratory, Columbia University RCV000681825 SCV000809300 likely pathogenic not provided 2018-09-16 no assertion criteria provided research

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