ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.1222C>T (p.Pro408Ser)

gnomAD frequency: 0.00006  dbSNP: rs201192228
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001062749 SCV001227568 uncertain significance Nephronophthisis 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 408 of the NPHP4 protein (p.Pro408Ser). This variant is present in population databases (rs201192228, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. ClinVar contains an entry for this variant (Variation ID: 857134). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt NPHP4 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV002479370 SCV002786382 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2022-01-18 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003906168 SCV004723671 uncertain significance NPHP4-related condition 2023-12-26 criteria provided, single submitter clinical testing The NPHP4 c.1222C>T variant is predicted to result in the amino acid substitution p.Pro408Ser. This variant has been reported to be maternally inherited in an individual with tetralogy of fallot (Table S3, Ekure et al. 2021. PubMed ID: 33448881). This variant is reported in 0.026% of alleles in individuals of African descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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