ClinVar

Description

Variant summary: LZTR1 c.372C>T alters a non-conserved nucleotide resulting in a synonymous change. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4e-05 in 251242 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in LZTR1 causing Noonan Syndrome 2 (4e-05 vs 0.0032), allowing no conclusion about variant significance. c.372C>T has been reported in the literature as a compound heterozygous genotype with another missense variant (c.509G>A, p.Arg170Gln) in at-least one individual affected with autosomal recessive LZTR1-related Noonan Syndrome (example, Alkaya_2021). The authors reported biparental inheritance and a likely pathogenic classification for this variant (ACMG PS3 and PM2 engaged) based on a transcript lacking exon 4 resulting in a premature stop codon (p.Arg108Glyfs*11). However, primary data supporting this outcome was not reported. An incomplete splicing effect resulting from alteration of an exonic splice enhancer resulting in a hypomorphic loss of function allele was proposed based on a personal communication with one of the authors of this study. These report(s) do not provide unequivocal conclusions about association of the variant with Noonan Syndrome 2 ( autosomal recessive LZTR1-related Noonan Syndrome). To our knowledge, no direct experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely benign. To our knowledge, the recent report utilized in the context of our evaluation was not considered. Based on the evidence outlined above, the variant was classified as uncertain significance.