ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.319-2A>G

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002975493 SCV003282751 likely pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2022-01-03 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. This variant has not been reported in the literature in individuals affected with SMPD1-related conditions. This variant is present in population databases (rs779080655, gnomAD 0.003%). This sequence change affects an acceptor splice site in intron 1 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).
Baylor Genetics RCV003465876 SCV004205508 likely pathogenic Niemann-Pick disease, type A 2023-05-04 criteria provided, single submitter clinical testing

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