ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.5813_5817del (p.Thr1938fs)

dbSNP: rs62638180
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000803171 SCV000943033 pathogenic Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis 2023-07-31 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 99861). This premature translational stop signal has been observed in individual(s) with Leber congenital amaurosis (LCA) (PMID: 16909394, 17705300, 20690115, 21153841). 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 sequence change creates a premature translational stop signal (p.Thr1938Asnfs*16) 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).
CeGaT Center for Human Genetics Tuebingen RCV000086299 SCV001246562 pathogenic not provided 2018-11-01 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002505021 SCV002810450 pathogenic Leber congenital amaurosis 10; Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 2022-03-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003467016 SCV004214878 pathogenic Bardet-Biedl syndrome 14 2023-12-19 criteria provided, single submitter clinical testing
Retina International RCV000086299 SCV000118445 not provided not provided no assertion provided not provided
Natera, Inc. RCV001826776 SCV002091861 pathogenic Leber congenital amaurosis 2021-02-05 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004529903 SCV004121514 pathogenic CEP290-related disorder 2024-09-11 no assertion criteria provided clinical testing The CEP290 c.5813_5817del5 variant is predicted to result in a frameshift and premature protein termination (p.Thr1938Asnfs*16). This variant has been reported in the compound heterozygous state with a recurrent deep intronic variant (c.2991+1655A>G) in multiple individuals with Leber Congenital Amaurosis (den Hollander et al. 2006. PubMed ID: 16909394; Frank et al. 2008. PubMed ID: 17705300; Wiszniewski et al. 2011. PubMed ID: 21153841; Testa et al. 2021. PubMed ID: 34196655). This variant is reported in 0.00081% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Frameshift variants in CEP290 are expected to be pathogenic. Given the evidence, we interpret c.5813_5817del (p.Thr1938Asnfs*16) as pathogenic.

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