ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.2830G>A (p.Val944Ile)

gnomAD frequency: 0.00010  dbSNP: rs188262700
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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) RCV000597571 SCV000709288 uncertain significance not provided 2017-12-13 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001050429 SCV001214536 uncertain significance Nephronophthisis 2024-12-09 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 944 of the NPHP4 protein (p.Val944Ile). This variant is present in population databases (rs188262700, 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: 502514). 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.
Ambry Genetics RCV004955706 SCV005464529 uncertain significance Inborn genetic diseases 2024-11-11 criteria provided, single submitter clinical testing The c.2830G>A (p.V944I) alteration is located in exon 21 (coding exon 20) of the NPHP4 gene. This alteration results from a G to A substitution at nucleotide position 2830, causing the valine (V) at amino acid position 944 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004732967 SCV005354265 uncertain significance NPHP4-related disorder 2024-03-28 no assertion criteria provided clinical testing The NPHP4 c.2830G>A variant is predicted to result in the amino acid substitution p.Val944Ile. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.017% of alleles in individuals of South Asian 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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