ClinVar Miner

Submissions for variant NM_025114.3(CEP290):c.5668G>T (p.Gly1890Ter) (rs137852832)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000086298 SCV000202411 pathogenic not provided 2014-05-01 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000515339 SCV000611257 pathogenic Leber congenital amaurosis 10; Meckel syndrome type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 2017-05-18 criteria provided, single submitter clinical testing
GeneDx RCV000086298 SCV000617621 pathogenic not provided 2018-05-08 criteria provided, single submitter clinical testing The G1890X variant in the CEP290 gene has been reported previously as homozygous and compound heterozygous in multiple individuals from three different families with clinical features of Joubert syndrome, including nephronophthisis (Sayer et al., 2006). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The G1890X variant is observed in 6/14472 (0.04%) alleles from individuals of South Asian background, in the ExAC dataset, and no individuals were reported to be homozygous (Lek et al., 2016). We interpret G1890X as a pathogenic variant.
Genetic Services Laboratory, University of Chicago RCV000114202 SCV000147755 pathogenic Meckel-Gruber syndrome 2013-07-22 criteria provided, single submitter clinical testing
Invitae RCV000531295 SCV000634661 pathogenic Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis 2018-12-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gly1890*) in the CEP290 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs137852832, ExAC 0.04%). This variant is one of the most commonly reported variants in individuals affected with Joubert syndrome (PMID: 16682970, 16682973, 17564967, 21068128, 22693042, 25818971, 26092869), many of whom are homozygous for this variant. It has also been reported in individuals affected with retinitis pigmentosa (PMID: 23591405, 27353947), Leber congenital amaurosis (PMID: 21245082, 22355252), and Meckel syndrome (PMID: 23954617). Loss-of-function variants in CEP290 are known to be pathogenic (PMID: 16909394, 17345604, 20690115). For these reasons, this variant has been classified as Pathogenic.
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet RCV000787813 SCV000926823 pathogenic Retinitis pigmentosa 2018-04-01 no assertion criteria provided research
OMIM RCV000001396 SCV000021546 pathogenic Joubert syndrome 5 2007-07-01 no assertion criteria provided literature only
Retina International RCV000086298 SCV000118444 not provided not provided no assertion provided not provided
UW Hindbrain Malformation Research Program,University of Washington RCV000001396 SCV000256366 pathogenic Joubert syndrome 5 2015-02-23 criteria provided, single submitter research

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