ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.1828C>T (p.Arg610Cys)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002971836 SCV003287246 likely pathogenic Niemann-Pick disease, type B; Niemann-Pick disease, type A 2024-01-25 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 610 of the SMPD1 protein (p.Arg610Cys). This variant is present in population databases (rs375915127, gnomAD 0.03%). This missense change has been observed in individual(s) with acid sphingomyelinase deficiency (PMID: 34660203). ClinVar contains an entry for this variant (Variation ID: 2073371). 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 with a positive predictive value of 95%. 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.
Revvity Omics, Revvity RCV003138419 SCV003822021 uncertain significance not provided 2021-10-25 criteria provided, single submitter clinical testing

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