ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.2714G>A (p.Ser905Asn)

gnomAD frequency: 0.00033  dbSNP: rs368298952
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000730347 SCV000858076 uncertain significance not provided 2018-03-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001070602 SCV001235863 uncertain significance Nephronophthisis 2025-01-29 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 905 of the NPHP4 protein (p.Ser905Asn). This variant is present in population databases (rs368298952, gnomAD 0.08%). 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: 594942). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt NPHP4 protein function with a negative predictive value of 80%. 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 RCV002499356 SCV002797106 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2022-01-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV002535153 SCV003738135 uncertain significance Inborn genetic diseases 2024-12-07 criteria provided, single submitter clinical testing The c.2714G>A (p.S905N) alteration is located in exon 20 (coding exon 19) of the NPHP4 gene. This alteration results from a G to A substitution at nucleotide position 2714, causing the serine (S) at amino acid position 905 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004535833 SCV004116510 uncertain significance NPHP4-related disorder 2022-08-23 criteria provided, single submitter clinical testing The NPHP4 c.2714G>A variant is predicted to result in the amino acid substitution p.Ser905Asn. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.080% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-5937256-C-T). 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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