ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.318+2T>C

dbSNP: rs1225462507
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000666977 SCV000791358 likely pathogenic Niemann-Pick disease, type A 2017-05-16 criteria provided, single submitter clinical testing
Invitae RCV001378222 SCV001575750 likely pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2023-12-21 criteria provided, single submitter clinical testing This sequence change affects a donor 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). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SMPD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 551827). 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.
Natera, Inc. RCV000666977 SCV002091673 likely pathogenic Niemann-Pick disease, type A 2020-05-05 no assertion criteria provided clinical testing

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