ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.2407-18G>A

gnomAD frequency: 0.00014  dbSNP: rs542841506
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001810660 SCV001477588 uncertain significance not provided 2020-03-03 criteria provided, single submitter clinical testing The LZTR1 c.2407-18G>A variant (rs542841506), to our knowledge, is not reported in the medical literature or gene specific databases. This variant is found in the general population with an overall allele frequency of 0.015% (42/280862 alleles) in the Genome Aggregation Database. This is an intronic variant in a weakly conserved nucleotide, but computational analyses (Alamut v.2.11) predict that this variant may impact splicing by creating a novel cryptic acceptor splice site. However, without functional studies the effect on splicing is unknown. Loss of function variants in LZTR1 are associated with autosomal recessive Noonan syndrome and schwannomatosis (Motta 2019, Pagnamenta 2019). Due to limited information, the clinical significance of the c.2407-18G>A variant is uncertain at this time. References: Motta M et al. Dominant Noonan syndrome-causing LZTR1 mutations specifically affect the Kelch domain substrate-recognition surface and enhance RAS-MAPK signaling. Hum Mol Genet. 2019 Mar 15;28(6):1007-1022. Pagnamenta AT et al. Delineation of dominant and recessive forms of LZTR1-associated Noonan syndrome. Clin Genet. 2019 Jun;95(6):693-703.
Labcorp Genetics (formerly Invitae), Labcorp RCV001810660 SCV002354539 likely benign not provided 2025-01-23 criteria provided, single submitter clinical testing
Baylor Genetics RCV003469504 SCV004193674 uncertain significance LZTR1-related schwannomatosis 2023-04-16 criteria provided, single submitter clinical testing

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