ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1091+1G>A

dbSNP: rs1847955457
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Huiwen Zhang's lab, Shanghai Jiao Tong University School of Medicine, Xinhua Hospital RCV001281414 SCV001468719 pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2020-12-30 criteria provided, single submitter clinical testing
Invitae RCV001281414 SCV001576888 likely pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2022-06-13 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 992698). Disruption of this splice site has been observed in individual(s) with Niemann-Pick disease (PMID: 33675270). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 2 of the SMPD1 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 SMPD1 are known to be pathogenic (PMID: 12369017, 15221801).

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