ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1406A>C (p.Tyr469Ser)

dbSNP: rs267607074
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001379382 SCV001577176 pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2022-10-11 criteria provided, single submitter clinical testing Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SMPD1 protein function. Experimental studies have shown that this missense change affects SMPD1 function (PMID: 19405096). For these reasons, this variant has been classified as Pathogenic. This missense change has been observed in individual(s) with Niemann-Pick A disease and/or Niemann-Pick B disease (PMID: 19405096, 30795770). ClinVar contains an entry for this variant (Variation ID: 2996). This variant is also known as Y467S. This sequence change replaces tyrosine, which is neutral and polar, with serine, which is neutral and polar, at codon 469 of the SMPD1 protein (p.Tyr469Ser). This variant is not present in population databases (gnomAD no frequency).
Baylor Genetics RCV000003131 SCV005052853 likely pathogenic Niemann-Pick disease, type A 2023-12-28 criteria provided, single submitter clinical testing
OMIM RCV000003131 SCV000023289 pathogenic Niemann-Pick disease, type A 2009-07-01 no assertion criteria provided literature only

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