ClinVar Miner

Submissions for variant NM_004525.3(LRP2):c.3667+1G>A

gnomAD frequency: 0.00001  dbSNP: rs752197557
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Daryl Scott Lab, Baylor College of Medicine RCV001269295 SCV001448641 likely pathogenic Donnai-Barrow syndrome 2020-11-11 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001269295 SCV002809863 likely pathogenic Donnai-Barrow syndrome 2021-11-01 criteria provided, single submitter clinical testing
Invitae RCV002541641 SCV003229302 likely pathogenic not provided 2023-11-02 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 24 of the LRP2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LRP2 are known to be pathogenic (PMID: 17632512, 25682901). This variant is present in population databases (rs752197557, gnomAD 0.003%). Disruption of this splice site has been observed in individual(s) with clinical features of Donnai-Barrow syndrome (PMID: 33461977). ClinVar contains an entry for this variant (Variation ID: 987893). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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