ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1487-4_1499del

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV003780012 SCV004603903 pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2023-12-14 criteria provided, single submitter clinical testing This variant results in the deletion of part of exon 6 (c.1487-4_1499del) of the SMPD1 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SMPD1-related conditions. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). This variant disrupts a region of the SMPD1 protein in which other variant(s) (p.Arg498His) have been determined to be pathogenic (PMID: 15221801, 27338287, 31965297, 32292456; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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