ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.2939C>T (p.Thr980Met)

gnomAD frequency: 0.00006  dbSNP: rs199645515
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000400326 SCV000343307 uncertain significance not provided 2016-06-21 criteria provided, single submitter clinical testing
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000791067 SCV000930337 uncertain significance not specified 2019-04-27 criteria provided, single submitter clinical testing
Invitae RCV001037539 SCV001200958 uncertain significance Nephronophthisis 2022-10-04 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 980 of the NPHP4 protein (p.Thr980Met). This variant is present in population databases (rs199645515, gnomAD 0.03%). 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: 289035). 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 RCV002494883 SCV002786663 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2022-03-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV002519317 SCV003662311 uncertain significance Inborn genetic diseases 2022-10-03 criteria provided, single submitter clinical testing The c.2939C>T (p.T980M) alteration is located in exon 21 (coding exon 20) of the NPHP4 gene. This alteration results from a C to T substitution at nucleotide position 2939, causing the threonine (T) at amino acid position 980 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
CeGaT Center for Human Genetics Tuebingen RCV000400326 SCV004701556 uncertain significance not provided 2024-02-01 criteria provided, single submitter clinical testing

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