ClinVar Miner

Submissions for variant NM_001298.3(CNGA3):c.1981C>A (p.Arg661Ser)

gnomAD frequency: 0.00012  dbSNP: rs183838250
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV001075514 SCV001241139 pathogenic Retinal dystrophy 2020-09-29 criteria provided, single submitter clinical testing
Invitae RCV001202143 SCV001373247 pathogenic not provided 2024-01-11 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 661 of the CNGA3 protein (p.Arg661Ser). This variant is present in population databases (rs183838250, gnomAD 0.2%). This missense change has been observed in individual(s) with clinical features of achromatopsia or cone-rod dystrophy (PMID: 24676353, 30711023; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 867037). 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 CNGA3 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001202143 SCV002522098 likely pathogenic not provided 2022-03-03 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30711023, 32141364, 24676353)

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