ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.320+5G>A

dbSNP: rs1555927336
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000519229 SCV000621297 uncertain significance not provided 2018-10-25 criteria provided, single submitter clinical testing The c.320+5G>A variant in the LZTR1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant reduces the quality of the splice donor site in intron 3, and is predicted to cause abnormal gene splicing resulting in an in-frame protein product with an abnormal message. However, in the absence of RNA/functional studies, the actual effect of c.320+5G>A is unknown. The c.320+5G>A variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.320+5G>A as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV000519229 SCV003281961 uncertain significance not provided 2022-10-01 criteria provided, single submitter clinical testing This sequence change falls in intron 3 of the LZTR1 gene. It does not directly change the encoded amino acid sequence of the LZTR1 protein. It affects a nucleotide within the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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: 452486). This variant has not been reported in the literature in individuals affected with LZTR1-related conditions. This variant is not present in population databases (gnomAD no frequency).
Baylor Genetics RCV003470659 SCV004193628 uncertain significance Schwannomatosis 2 2023-06-27 criteria provided, single submitter clinical testing

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