Identification of novel JAK3 variants in a suspected SCID patient and two couples undergoing carrier screening

Severe combined immunodeficiency (SCID) is one of the most severe forms of primary immunodeficiency. JAK3 gene is a critical determinant of SCID, as JAK3-STAT pathway regulates development, proliferation, activation, and differentiation of immune cells. This study aimed to identify the genetic cause of a family with a suspected SCID patient, and to perform carrier screening for two couples to assess the risk of conceiving offspring with birth defects.

Whole-Exome Sequencing was performed on five individuals from the three families. A series of in vitro functional experiments, including Western blotting and luciferase assays, were conducted to assess the pathogenicity of the identified JAK3 variants.

We identified seven JAK3 variants, including five variants of uncertain significance (p.Arg402His, p.ILe688Phe, p.Leu129Phe, p.Met235Thr, p.Ala634Pro) and one pathogenic variant and one likely pathogenic variant (p.Gln1007Ter and p.Cys376Leufs*34). Among these, four variants (p.Gln1007Ter, p.Leu129Phe, p.Cys376Leufs*34 and p.Ala634Pro) were novel. In vitro functional experiments revealed that three of five variants of uncertain significance (VUSs) significantly reduced STAT5 phosphorylation and transcriptional activity, thereby reclassifying two variants (p.Arg402His and p.ILe688Phe) as likely pathogenic variants (LP) and one variant (p.Leu129Phe) as VUS with a Bayesian score of 3. In contrast, the remaining two variants (p.Ala634Pro and p.Met235Thr) did not affect JAK3 function, and were reclassified as VUS with a Bayesian score of 1 or 0.

This study identified seven JAK3 variants from three families, including four novel variants. Functional experiments revealed that two VUSs were reclassified as LP and one VUS were reclassified as VUS with a Bayesian score of 3. These findings highlight the importance of integrating genetic and functional analyses to enhance diagnostic accuracy, inform treatment strategies for patients, clarify of the risk for carrier-screening couples, improve genetic counseling, and guide reproductive interventions.