ClinVar Miner

Submissions for variant NM_001298.3(CNGA3):c.778G>A (p.Asp260Asn)

gnomAD frequency: 0.00003  dbSNP: rs374258471
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000850497 SCV000992697 likely pathogenic Achromatopsia 2 2018-10-12 criteria provided, single submitter clinical testing
Blueprint Genetics RCV001073600 SCV001239151 pathogenic Retinal dystrophy 2019-07-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001384601 SCV001584158 pathogenic not provided 2024-02-18 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 260 of the CNGA3 protein (p.Asp260Asn). This variant is present in population databases (rs374258471, gnomAD 0.006%). This missense change has been observed in individual(s) with CNGA3-related conditions (PMID: 11536077, 24903488, 26992781, 28159970, 30682209). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 689726). 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%. Experimental studies have shown that this missense change affects CNGA3 function (PMID: 17693388). For these reasons, this variant has been classified as Pathogenic.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001384601 SCV001905544 pathogenic not provided 2021-09-15 criteria provided, single submitter clinical testing
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg RCV001073600 SCV005068392 pathogenic Retinal dystrophy 2023-01-01 criteria provided, single submitter clinical testing
GeneDx RCV001384601 SCV005421324 pathogenic not provided 2024-06-03 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect: damaged cone photoreceptor cGMP-gated cation channel (PMID: 17693388); 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: 24676353, 26992781, 28159970, 31216405, 11536077, 30682209, 25637600, 19592100, 31964843, 34360608, 35332618, 32531858, 24903488, 35119454, 37372476, 37734845, 17693388)

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