ClinVar Miner

Submissions for variant NM_001298.3(CNGA3):c.1717T>C (p.Tyr573His)

gnomAD frequency: 0.00001  dbSNP: rs1330420689
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001865864 SCV002307455 pathogenic not provided 2024-04-25 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 573 of the CNGA3 protein (p.Tyr573His). This variant is present in population databases (no rsID available, gnomAD 0.06%). This missense change has been observed in individual(s) with clinical features of achromatopsia (PMID: 35332618; 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: 1064475). 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%. This variant disrupts the p.Tyr573 amino acid residue in CNGA3. Other variant(s) that disrupt this residue have been observed in individuals with CNGA3-related conditions (PMID: 11536077; Invitae), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Mendelics RCV001729876 SCV002518729 pathogenic Achromatopsia 2 2022-05-04 criteria provided, single submitter clinical testing
Molecular Genetics Laboratory, Institute for Ophthalmic Research RCV001729876 SCV001571309 likely pathogenic Achromatopsia 2 2021-04-15 no assertion criteria provided research

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