ClinVar Miner

Submissions for variant NM_002185.5(IL7R):c.380T>G (p.Val127Gly)

dbSNP: rs751109965
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001053850 SCV001218132 uncertain significance Immunodeficiency 104 2024-01-19 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 127 of the IL7R protein (p.Val127Gly). This variant is present in population databases (rs751109965, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with IL7R-related conditions. ClinVar contains an entry for this variant (Variation ID: 849816). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
Neuberg Centre For Genomic Medicine, NCGM RCV001053850 SCV005329514 uncertain significance Immunodeficiency 104 2023-05-20 criteria provided, single submitter clinical testing The observed missense c.380T>G(p.Val127Gly) variant in IL7R gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is reported with the allele frequency of 0.003% in the gnomAD Exomes. This variant has been reported to the ClinVar database as Uncertain Significance. However, no details are available for independent assessment. The amino acid Val at position 127 is changed to a Gly changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Val127Gly in IL7R is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Multiple lines of computational evidence (Polyphen - Damaging, SIFT - Damaging and MutationTaster - Disease causing) predict a damaging effect on protein structure and function for this variant. For these reasons, this variant has been classified as Uncertain Significance.

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