ClinVar Miner

Submissions for variant NM_000350.3(ABCA4):c.5460+1G>A

dbSNP: rs61753030
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
The Cell Therapy Center, The University of Jordan RCV000791319 SCV000920579 pathogenic Retinitis pigmentosa 2019-03-15 criteria provided, single submitter research The splice site donor variant ABCA4 (c.5460+1G>A) was found in two unrelated Jordanian families and clinical evaluation showed that one of them has retinitis pigmentosa (rod-cone dystrophy) and the other has cone-rod dystrophy. This variant has been found in the proband by exome sequencing and segregates with the disease in both families. Multiple in-silico tools predicted this variant to affect splicing causing exon skipping resulting in out of frame transcript.
Labcorp Genetics (formerly Invitae), Labcorp RCV000085729 SCV002247409 pathogenic not provided 2022-08-22 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 99375). Disruption of this splice site has been observed in individuals with inherited retinal dystrophy (PMID: 26593885, 31968401). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 38 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).
Retina International RCV000085729 SCV000117869 not provided not provided no assertion provided not provided
Sharon lab, Hadassah-Hebrew University Medical Center RCV001002813 SCV001160827 pathogenic Stargardt disease 2019-06-23 no assertion criteria provided research
Faculty of Health Sciences, Beirut Arab University RCV001257848 SCV001434615 pathogenic Autosomal recessive retinitis pigmentosa 2020-01-22 no assertion criteria provided literature only

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