ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.1261-2A>G

gnomAD frequency: 0.00001  dbSNP: rs759240190
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001769173 SCV002003301 uncertain significance not provided 2020-10-14 criteria provided, single submitter clinical testing Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Has not been previously published as pathogenic or benign to our knowledge
Baylor Genetics RCV003470887 SCV004193665 uncertain significance Schwannomatosis 2 2023-05-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001769173 SCV004270025 likely pathogenic not provided 2022-11-24 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1313222). This variant has not been reported in the literature in individuals affected with LZTR1-related conditions. This variant is present in population databases (rs759240190, gnomAD 0.03%). This sequence change affects an acceptor splice site in intron 11 of the LZTR1 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 LZTR1 are known to be pathogenic (PMID: 24362817, 25335493, 25480913, 25795793, 29469822, 30368668, 30442762, 30442766, 30481304, 30859559).

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