ClinVar Miner

Submissions for variant NM_000543.5(SMPD1):c.58G>A (p.Gly20Arg)

gnomAD frequency: 0.00003  dbSNP: rs538153468
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000729102 SCV000856741 uncertain significance not provided 2017-09-05 criteria provided, single submitter clinical testing
Invitae RCV002535106 SCV003483030 uncertain significance Niemann-Pick disease, type B; Niemann-Pick disease, type A 2022-08-02 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 20 of the SMPD1 protein (p.Gly20Arg). This variant is present in population databases (rs538153468, gnomAD 0.01%). 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: 593927). 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 not expected to disrupt SMPD1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
PreventionGenetics, part of Exact Sciences RCV003420290 SCV004107251 uncertain significance SMPD1-related disorder 2023-06-12 criteria provided, single submitter clinical testing The SMPD1 c.58G>A variant is predicted to result in the amino acid substitution p.Gly20Arg. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.013% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-6411886-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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