ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.2851C>T (p.Arg951Ter)

gnomAD frequency: 0.00004  dbSNP: rs148670389
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001205716 SCV001376986 pathogenic Nephronophthisis 2022-07-22 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg951*) 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). 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: 936828). This premature translational stop signal has been observed in individual(s) with NPHP3-related conditions (Invitae). This variant is present in population databases (rs148670389, gnomAD 0.006%).
Fulgent Genetics, Fulgent Genetics RCV002504239 SCV002807969 likely pathogenic Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-12-09 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004528417 SCV004106016 likely pathogenic NPHP3-related disorder 2024-01-05 criteria provided, single submitter clinical testing The NPHP3 c.2851C>T variant is predicted to result in premature protein termination (p.Arg951*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD. Nonsense variants in NPHP3 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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