ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.1049C>T (p.Pro350Leu)

gnomAD frequency: 0.00006  dbSNP: rs201129306
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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 RCV001925974 SCV002178399 uncertain significance Sphingolipid activator protein 1 deficiency 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 350 of the PSAP protein (p.Pro350Leu). This variant is present in population databases (rs201129306, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with PSAP-related conditions. ClinVar contains an entry for this variant (Variation ID: 1413486). 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 PSAP 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.
GeneDx RCV003229903 SCV003927719 uncertain significance not provided 2022-11-28 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Baylor Genetics RCV003333191 SCV004041010 uncertain significance Combined PSAP deficiency 2023-03-01 criteria provided, single submitter clinical testing

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