ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3111C>G (p.Tyr1037Ter)

gnomAD frequency: 0.00001  dbSNP: rs1007848349
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001220697 SCV001392704 pathogenic Nephronophthisis 2022-06-04 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 949269). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr1037*) 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).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002298907 SCV002599019 likely pathogenic Joubert syndrome and related disorders 2022-09-20 criteria provided, single submitter clinical testing Variant summary: NPHP3 c.3111C>G (p.Tyr1037X) 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 in ClinVar database. The variant was absent in 250172 control chromosomes (gnomAD). To our knowledge, no occurrence of c.3111C>G in individuals affected with Joubert Syndrome And Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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