ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3032C>T (p.Ala1011Val)

gnomAD frequency: 0.00006  dbSNP: rs202145723
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000593437 SCV000704656 uncertain significance not provided 2016-12-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001056390 SCV001220831 uncertain significance Nephronophthisis 2022-07-12 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1011 of the NPHP3 protein (p.Ala1011Val). This variant is present in population databases (rs202145723, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 499254). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000593437 SCV002542072 uncertain significance not provided 2021-10-20 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002476302 SCV002790543 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-04-02 criteria provided, single submitter clinical testing
GeneDx RCV000593437 SCV003926420 uncertain significance not provided 2022-11-21 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004024761 SCV004990285 uncertain significance Inborn genetic diseases 2023-11-17 criteria provided, single submitter clinical testing The c.3032C>T (p.A1011V) alteration is located in exon 21 (coding exon 21) of the NPHP3 gene. This alteration results from a C to T substitution at nucleotide position 3032, causing the alanine (A) at amino acid position 1011 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004740352 SCV005347696 uncertain significance NPHP3-related disorder 2024-04-08 no assertion criteria provided clinical testing The NPHP3 c.3032C>T variant is predicted to result in the amino acid substitution p.Ala1011Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.031% 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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