ClinVar Miner

Submissions for variant NM_000350.3(ABCA4):c.4539+1G>T

dbSNP: rs61751388
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001723666 SCV001950195 pathogenic Retinitis pigmentosa 2021-04-01 criteria provided, single submitter curation The c.4539+1G>T variant in ABCA4 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3-P. Based on this evidence we have classified this variant as Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab.
Labcorp Genetics (formerly Invitae), Labcorp RCV000085647 SCV003523416 pathogenic not provided 2023-09-27 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 30 of the ABCA4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ABCA4 are known to be pathogenic (PMID: 10958761, 24938718, 25312043, 26780318). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Stargardt disease, cone-rod dystrophy, or retinitis pigmentosa (PMID: 9466990). 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: 99294). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000008343 SCV000028551 pathogenic Retinitis pigmentosa 19 1998-03-01 no assertion criteria provided literature only
OMIM RCV000008344 SCV000028552 pathogenic Cone-rod dystrophy 3 1998-03-01 no assertion criteria provided literature only
Retina International RCV000085647 SCV000117786 not provided not provided no assertion provided not provided
Clinical Genetics, Academic Medical Center RCV000085647 SCV001919335 pathogenic not provided no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000085647 SCV001952336 pathogenic not provided no assertion criteria provided clinical testing

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