ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.406del (p.Thr136fs)

dbSNP: rs1379989124
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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) RCV000734775 SCV000862944 pathogenic not provided 2018-08-17 criteria provided, single submitter clinical testing
Blueprint Genetics RCV000734775 SCV000927974 likely pathogenic not provided 2018-10-05 criteria provided, single submitter clinical testing
Invitae RCV001228010 SCV001400391 pathogenic Nephronophthisis 2022-11-15 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: 598394). This premature translational stop signal has been observed in individual(s) with nephronophthisis (PMID: 23188109). This variant is present in population databases (no rsID available, gnomAD 0.004%). This sequence change creates a premature translational stop signal (p.Thr136Argfs*13) 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).
PreventionGenetics, part of Exact Sciences RCV004527767 SCV004107842 pathogenic NPHP3-related disorder 2022-12-19 criteria provided, single submitter clinical testing The NPHP3 c.406delA variant is predicted to result in a frameshift and premature protein termination (p.Thr136Argfs*13). This variant was reported in the homozygous state in an individual with infantile nephronophthisis (Halbritter et al 2012. PubMed ID: 23188109). This variant is reported in 0.0041% of alleles in individuals of African descent in gnomAD ( Frameshift variants in NPHP3 are expected to be pathogenic. This variant is interpreted as pathogenic.

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