ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.1199C>T (p.Thr400Ile)

dbSNP: rs773578133
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000526103 SCV000634635 uncertain significance Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis 2022-09-27 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 400 of the CEP290 protein (p.Thr400Ile). This variant is present in population databases (rs773578133, gnomAD 0.05%). This missense change has been observed in individuals with CEP290-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 461773). 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 not expected to disrupt CEP290 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.
GeneDx RCV000839270 SCV000981164 likely benign not provided 2018-04-27 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
PreventionGenetics, part of Exact Sciences RCV003419940 SCV004113986 uncertain significance CEP290-related condition 2024-02-20 criteria provided, single submitter clinical testing The CEP290 c.1199C>T variant is predicted to result in the amino acid substitution p.Thr400Ile. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.050% of alleles in individuals of Latino descent in gnomAD, which is likely too common for a primary cause of disease. Although we suspect this variant may be benign, at this time, the clinical significance is uncertain due to the absence of conclusive functional and genetic evidence.

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