ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.1027A>G (p.Ile343Val)

gnomAD frequency: 0.00003  dbSNP: rs372145755
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000252767 SCV000316254 likely benign not specified criteria provided, single submitter clinical testing
Invitae RCV001038847 SCV001202346 uncertain significance Nephronophthisis 2019-12-31 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 262691). This variant is present in population databases (rs372145755, ExAC 0.03%). This sequence change replaces isoleucine with valine at codon 343 of the NPHP3 protein (p.Ile343Val). The isoleucine residue is moderately conserved and there is a small physicochemical difference between isoleucine and valine. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies.

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