ClinVar Miner

Submissions for variant NM_002778.4(PSAP):c.645C>A (p.Asn215Lys)

gnomAD frequency: 0.00002  dbSNP: rs770171865
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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 RCV001063288 SCV001228126 pathogenic Sphingolipid activator protein 1 deficiency 2023-09-13 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as 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 PSAP protein function. ClinVar contains an entry for this variant (Variation ID: 857581). This missense change has been observed in individual(s) with atypical metachromatic leukodystrophy due to saposin B deficiency (PMID: 10196694, 17616409, 18693274, 26462614). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs770171865, gnomAD 0.006%). This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 215 of the PSAP protein (p.Asn215Lys).
Natera, Inc. RCV001827403 SCV002087042 likely pathogenic Metachromatic leukodystrophy 2020-08-15 no assertion criteria provided clinical testing

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