ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1297T>C (p.Cys433Arg)

gnomAD frequency: 0.00001  dbSNP: rs779528546
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001004366 SCV001163306 likely pathogenic Niemann-Pick disease, type A criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002549241 SCV003439785 likely pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2022-04-05 criteria provided, single submitter clinical testing This variant is present in population databases (rs779528546, gnomAD 0.0009%). 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. 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. ClinVar contains an entry for this variant (Variation ID: 813420). This variant is also known as C431R. This missense change has been observed in individual(s) with SMPD1-related conditions (PMID: 12369017, 27338287). This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 433 of the SMPD1 protein (p.Cys433Arg).

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