ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.5587-1G>C

gnomAD frequency: 0.00001  dbSNP: rs968692633
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV001073923 SCV001239488 pathogenic Retinal dystrophy 2018-06-24 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001090823 SCV001246564 pathogenic not provided 2020-08-01 criteria provided, single submitter clinical testing
Invitae RCV001244155 SCV001417357 pathogenic Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis 2023-07-06 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: 636006). This sequence change affects an acceptor splice site in intron 40 of the CEP290 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 CEP290 are known to be pathogenic (PMID: 16909394, 17345604, 20690115). This variant is present in population databases (no rsID available, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with Joubert syndrome, Leber congenital amaurosis, or retinitis pigmentosa (PMID: 17345604, 28559085, 29178642).
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001090823 SCV001446874 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
GeneDx RCV001090823 SCV001756784 pathogenic not provided 2020-11-18 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame deletion of a critical region; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31734136, 28559085, 29178642, 17564967, 17345604, 25525159, 30718709)
Fulgent Genetics, Fulgent Genetics RCV002493435 SCV002797483 pathogenic Leber congenital amaurosis 10; Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 2022-04-12 criteria provided, single submitter clinical testing
Baylor Genetics RCV003467318 SCV004216566 pathogenic Bardet-Biedl syndrome 14 2023-08-10 criteria provided, single submitter clinical testing
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet RCV000787560 SCV000926536 pathogenic Leber congenital amaurosis 2018-04-01 no assertion criteria provided research
Natera, Inc. RCV000787560 SCV002091863 pathogenic Leber congenital amaurosis 2020-08-18 no assertion criteria provided clinical testing

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