ClinVar Miner

Submissions for variant NM_015272.5(RPGRIP1L):c.3121A>T (p.Lys1041Ter)

gnomAD frequency: 0.00001  dbSNP: rs1456208953
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001231979 SCV001404518 pathogenic Familial aplasia of the vermis; Meckel-Gruber syndrome 2023-04-26 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 create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 958759). This variant has not been reported in the literature in individuals affected with RPGRIP1L-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys1041*) in the RPGRIP1L gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RPGRIP1L are known to be pathogenic (PMID: 17558409).
Fulgent Genetics, Fulgent Genetics RCV002497792 SCV002813944 likely pathogenic Joubert syndrome 7; Meckel syndrome, type 5; COACH syndrome 3 2022-04-01 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004538486 SCV004116169 likely pathogenic RPGRIP1L-related disorder 2023-12-04 no assertion criteria provided clinical testing The RPGRIP1L c.3121A>T variant is predicted to result in premature protein termination (p.Lys1041*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in RPGRIP1L are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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