ClinVar Miner

Submissions for variant NM_001278116.2(L1CAM):c.1672C>T (p.Arg558Ter)

dbSNP: rs1557091773
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000579326 SCV000680538 pathogenic not provided 2021-06-09 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 10797421, 25525159, 19641926, 9195224, 27535533)
Labcorp Genetics (formerly Invitae), Labcorp RCV001044106 SCV001207882 pathogenic Spastic paraplegia 2019-12-27 criteria provided, single submitter clinical testing Loss-of-function variants in L1CAM are known to be pathogenic (PMID: 19846429). For these reasons, this variant has been classified as Pathogenic. This variant has been observed in individuals affected with L1CAM-related conditions (PMID: 9195224, 19641926, 10797421). ClinVar contains an entry for this variant (Variation ID: 488700). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg558*) in the L1CAM gene. It is expected to result in an absent or disrupted protein product.
DASA RCV002298692 SCV002588757 pathogenic MASA syndrome 2022-11-03 criteria provided, single submitter clinical testing The c.1672C>T;p.(Arg558*) variant creates a premature translational stop signal in the L1CAM gene. It is expected to result in an absent or disrupted protein product - PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 488700; PMID: 19641926; 9300653; 10797421; 9195224) - PS4. This variant is not present in population databases (rs1557091773, gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. In summary, the currently available evidence indicates that the variant is pathogenic.

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