ClinVar Miner

Submissions for variant NM_000235.4(LIPA):c.398del (p.Leu132_Ser133insTer)

gnomAD frequency: 0.00008  dbSNP: rs756016704
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000368412 SCV000344457 pathogenic not provided 2018-01-09 criteria provided, single submitter clinical testing
Invitae RCV001376636 SCV000941771 pathogenic Wolman disease 2023-11-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser133*) in the LIPA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LIPA are known to be pathogenic (PMID: 23485521). This variant is present in population databases (rs756016704, gnomAD 0.004%). This premature translational stop signal has been observed in individuals with Wolman disease (PMID: 24832708, 28220406). ClinVar contains an entry for this variant (Variation ID: 289986). For these reasons, this variant has been classified as Pathogenic.
Centre for Inherited Metabolic Diseases, Karolinska University Hospital RCV000801965 SCV001554463 pathogenic Lysosomal acid lipase deficiency 2021-04-07 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000801965 SCV002060124 pathogenic Lysosomal acid lipase deficiency 2021-11-08 criteria provided, single submitter clinical testing NM_000235.2(LIPA):c.398delC(S133*) is a nonsense variant classified as pathogenic in the context of lysosomal acid lipase deficiency. S133* has been observed in cases with relevant disease (PMID: 11441129). Functional assessments of this variant are available in the literature (PMID: 11441129). S133* has been observed in population frequency databases (gnomAD: NFE 0.004%). In summary, NM_000235.2(LIPA):c.398delC(S133*) is a nonsense variant in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
Fulgent Genetics, Fulgent Genetics RCV000801965 SCV002813880 pathogenic Lysosomal acid lipase deficiency 2022-02-02 criteria provided, single submitter clinical testing
Natera, Inc. RCV000801965 SCV001453548 pathogenic Lysosomal acid lipase deficiency 2020-09-16 no assertion criteria provided clinical testing

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