ClinVar Miner

Submissions for variant NM_001005373.4(LRSAM1):c.2047-1G>A

dbSNP: rs1564287793
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000034318 SCV000813858 pathogenic Charcot-Marie-Tooth disease axonal type 2P 2022-05-27 criteria provided, single submitter clinical testing This sequence change falls in intron 24 of the LRSAM1 gene. It does not directly change the encoded amino acid sequence of the LRSAM1 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with autosomal dominant Charcot-Marie-Tooth disease (PMID: 22781092, 28286897). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 41418). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects LRSAM1 function (PMID: 29845787). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in activation of a cryptic splice site and introduces a new termination codon (PMID: 22781092). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000034318 SCV000058269 pathogenic Charcot-Marie-Tooth disease axonal type 2P 2013-02-01 no assertion criteria provided literature only
Inherited Neuropathy Consortium RCV000789359 SCV000928714 uncertain significance Charcot-Marie-Tooth disease no assertion criteria provided literature only

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