ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1486+5G>C

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Revvity Omics, Revvity RCV003138543 SCV003822017 uncertain significance not provided 2020-10-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003778789 SCV004570146 likely pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2023-08-08 criteria provided, single submitter clinical testing This sequence change falls in intron 5 of the SMPD1 gene. It does not directly change the encoded amino acid sequence of the SMPD1 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has been observed in individuals with Niemann-Pick disease (PMID: 23356216, 33675270, 33763395). ClinVar contains an entry for this variant (Variation ID: 2436206). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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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