ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.634dup (p.Glu212fs)

dbSNP: rs747052534
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000597690 SCV000707032 pathogenic not provided 2018-07-05 criteria provided, single submitter clinical testing
Invitae RCV001854072 SCV002230435 pathogenic Nephronophthisis 2022-08-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu212Glyfs*3) 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 (rs747052534, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 500889). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV002506426 SCV002815343 likely pathogenic Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-08-10 criteria provided, single submitter clinical testing
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV003336089 SCV004046109 likely pathogenic NPHP3-related disorder criteria provided, single submitter clinical testing This frameshifting variant in exon 3 of 27 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has not been previously reported or functionally characterized in the literature to our knowledge. Loss-of-function variants have been reported in individuals with NPHP3-related disorders (PMID: 32596782). The c.634dup (p.Glu212GlyfsTer3) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.001% (2/251454) and thus is presumed to be rare. Based on the available evidence, the c.634dup (p.Glu212GlyfsTer3) variant is classified as Likely Pathogenic.

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