ClinVar Miner

Submissions for variant NM_001005373.4(LRSAM1):c.175-2A>T

dbSNP: rs1035054313
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001197856 SCV001368639 uncertain significance Charcot-Marie-Tooth disease axonal type 2P 2019-10-22 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2,PP3.
Invitae RCV001197856 SCV004476216 likely pathogenic Charcot-Marie-Tooth disease axonal type 2P 2023-02-11 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 4 of the LRSAM1 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 LRSAM1 are known to be pathogenic (PMID: 20865121, 33414056). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LRSAM1-related conditions. ClinVar contains an entry for this variant (Variation ID: 931367). 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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