ClinVar Miner

Submissions for variant NM_000235.4(LIPA):c.822+1G>A

gnomAD frequency: 0.00001  dbSNP: rs1204744283
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665567 SCV000789713 likely pathogenic Lysosomal acid lipase deficiency 2017-02-14 criteria provided, single submitter clinical testing
Invitae RCV003495169 SCV004268391 likely pathogenic Wolman disease 2024-01-11 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 7 of the LIPA gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LIPA are known to be pathogenic (PMID: 23485521). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with LIPA-related conditions. ClinVar contains an entry for this variant (Variation ID: 550739). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

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