ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.6869dup (p.Asn2290fs)

dbSNP: rs587783017
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000457302 SCV000541578 pathogenic Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis 2023-11-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Asn2290Lysfs*6) in the CEP290 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CEP290 are known to be pathogenic (PMID: 16909394, 17345604, 20690115). 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 premature translational stop signal has been observed in individual(s) with Leber congenital amaurosis (PMID: 25445212). This variant is also known as c.6869_6870insA. ClinVar contains an entry for this variant (Variation ID: 156386). For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001075551 SCV001241177 pathogenic Retinal dystrophy 2018-12-20 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002271421 SCV002556284 pathogenic CEP290-Related Disorders 2022-06-30 criteria provided, single submitter clinical testing Variant summary: CEP290 c.6869dupA (p.Asn2290LysfsX6) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 0.00027 in 161872 control chromosomes. c.6869dupA has been reported in the literature in individuals affected with CEP290-Related Disorders. These data indicate that the variant may be associated with disease. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Fulgent Genetics, Fulgent Genetics RCV002483278 SCV002790486 pathogenic Leber congenital amaurosis 10; Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 2021-11-03 criteria provided, single submitter clinical testing
Baylor Genetics RCV003467204 SCV004214864 pathogenic Bardet-Biedl syndrome 14 2023-10-16 criteria provided, single submitter clinical testing
Molecular Diagnostics Laboratory, Seoul National University Hospital RCV000144468 SCV000189603 pathogenic Leber congenital amaurosis 10 2014-09-18 no assertion criteria provided clinical testing
Natera, Inc. RCV001276483 SCV001462862 pathogenic Leber congenital amaurosis 2020-09-16 no assertion criteria provided clinical testing

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