ClinVar Miner

Submissions for variant NM_000235.4(LIPA):c.1024G>A (p.Gly342Arg)

gnomAD frequency: 0.00003  dbSNP: rs776472526
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000671138 SCV000796088 likely pathogenic Lysosomal acid lipase deficiency 2017-12-01 criteria provided, single submitter clinical testing
Invitae RCV001376593 SCV001410727 pathogenic Wolman disease 2021-10-18 criteria provided, single submitter clinical testing This sequence change replaces glycine with arginine at codon 342 of the LIPA protein (p.Gly342Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine. This variant is present in population databases (rs776472526, ExAC 0.006%). This missense change has been observed in individuals with LIPA-related conditions (PMID: 10562460, 23485521, 24048164, 28881270). ClinVar contains an entry for this variant (Variation ID: 555337). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects LIPA function (PMID: 10562460). This variant disrupts the p.Gly342 amino acid residue in LIPA. Other variant(s) that disrupt this residue have been observed in individuals with LIPA-related conditions (PMID: 9925650), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Natera, Inc. RCV000671138 SCV002088969 pathogenic Lysosomal acid lipase deficiency 2020-06-25 no assertion criteria provided clinical testing

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