ClinVar Miner

Submissions for variant NM_000235.4(LIPA):c.1070T>C (p.Leu357Pro)

gnomAD frequency: 0.00001  dbSNP: rs772684869
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000667739 SCV000792238 uncertain significance Lysosomal acid lipase deficiency 2017-06-12 criteria provided, single submitter clinical testing
Alexion Pharmaceuticals, Inc RCV000667739 SCV000999841 likely pathogenic Lysosomal acid lipase deficiency 2019-06-01 criteria provided, single submitter research
Invitae RCV001379331 SCV001577117 likely pathogenic Wolman disease 2024-01-17 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 357 of the LIPA protein (p.Leu357Pro). This variant is present in population databases (rs772684869, gnomAD 0.008%). This missense change has been observed in individual(s) with cholesteryl ester storage disease (PMID: 7773732). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as Leu336Pro. ClinVar contains an entry for this variant (Variation ID: 552474). 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 LIPA protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects LIPA function (PMID: 7499245, 31131398, 31180157). 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.
Natera, Inc. RCV000667739 SCV002088925 likely pathogenic Lysosomal acid lipase deficiency 2020-07-09 no assertion criteria provided clinical testing

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