ClinVar Miner

Submissions for variant NM_000350.3(ABCA4):c.5065T>C (p.Ser1689Pro)

dbSNP: rs61753020
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg RCV000408570 SCV000281911 likely pathogenic Severe early-childhood-onset retinal dystrophy 2016-01-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000085695 SCV003523414 pathogenic not provided 2024-01-22 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 1689 of the ABCA4 protein (p.Ser1689Pro). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with Stargardt disease (PMID: 10958763, 28559085; 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: 99342). 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 ABCA4 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg RCV004815119 SCV005069945 likely pathogenic Retinal dystrophy 2022-01-01 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000408570 SCV005368345 uncertain significance Severe early-childhood-onset retinal dystrophy 2020-01-17 criteria provided, single submitter clinical testing Criteria applied: PM2,PM3
Retina International RCV000085695 SCV000117835 not provided not provided no assertion provided not provided

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