ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.1381G>T (p.Glu461Ter)

gnomAD frequency: 0.00002  dbSNP: rs119456961
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001197494 SCV001368260 pathogenic NPHP3-related Meckel-like syndrome 2019-09-23 criteria provided, single submitter clinical testing This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1.
Invitae RCV001389821 SCV001591309 pathogenic Nephronophthisis 2023-10-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu461*) in the NPHP3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHP3 are known to be pathogenic (PMID: 18371931, 23559409). This variant is present in population databases (rs119456961, gnomAD 0.004%). This premature translational stop signal has been observed in individual(s) with nephronophthisis (PMID: 12872122, 21866095). ClinVar contains an entry for this variant (Variation ID: 2634). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV002496236 SCV002778639 pathogenic Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-03-31 criteria provided, single submitter clinical testing
GeneDx RCV000681680 SCV004034548 pathogenic not provided 2023-03-06 criteria provided, single submitter clinical testing Nonsense 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 at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 21866095, 30586318, 36090483, 12872122)
OMIM RCV000002752 SCV000022910 pathogenic Nephronophthisis 3 2003-08-01 no assertion criteria provided literature only
Gharavi Laboratory, Columbia University RCV000681680 SCV000809127 pathogenic not provided 2018-09-16 no assertion criteria provided research

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