ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.369del (p.Gln123fs)

dbSNP: rs773622064
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001008847 SCV001168652 likely pathogenic not provided 2018-12-20 criteria provided, single submitter clinical testing The c.369delA variant in the CEP290 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.369delA variant causes a frameshift starting with codon Glutamine 123, changes this amino acid to a Histidine residue, and creates a premature Stop codon at position 2 of the new reading frame, denoted p.Gln123HisfsX2. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.369delA variant is observed in 4/24008 (0.017%) alleles from individuals of African background in large population cohorts (Lek et al., 2016). We interpret c.369delA as a likely pathogenic variant.
Invitae RCV001388565 SCV001589599 pathogenic Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis 2023-12-19 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln123Hisfs*2) 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). This variant is present in population databases (rs773622064, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CEP290-related conditions. ClinVar contains an entry for this variant (Variation ID: 817646). 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.
Fulgent Genetics, Fulgent Genetics RCV002481816 SCV002789619 likely pathogenic Leber congenital amaurosis 10; Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 2022-03-30 criteria provided, single submitter clinical testing
Baylor Genetics RCV003467587 SCV004216599 pathogenic Bardet-Biedl syndrome 14 2023-07-10 criteria provided, single submitter clinical testing

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