ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.1689G>A (p.Glu563=)

gnomAD frequency: 0.00001  dbSNP: rs977829129
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002138661 SCV002457651 likely benign not provided 2024-01-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV002400364 SCV002712685 likely benign Hereditary cancer-predisposing syndrome; Cardiovascular phenotype 2021-05-26 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV003325239 SCV004031240 uncertain significance Noonan syndrome 10 2023-07-25 criteria provided, single submitter clinical testing The LZTR1 c.1689G>A (p.Glu563=) synonymous change has a maximum frequency of 0.0028% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). Algorithms that predict the impact of sequence changes on splicing indicate that this change may impact splicing, but to our knowledge these predictions have not been confirmed by RNA studies. To our knowledge, this variant has not been reported in the literature in individuals with LZTR1-related disease. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.??

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