Variant summary: RAG1 c.1519C>T (p.Arg507Trp) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251076 control chromosomes. c.1519C>T has been reported in the literature as a compound heterozygous genotype in at-least two individuals with features of atypical Severe Combined Immunodeficiency Syndrome/Omenn Syndrome (SCID/OS) (example, Villa_2001, Schuetz_2008). One of these reported cases harbored this variant in cis with p.Arg737His on the paternal allele while the maternal allele harbored a different variant (p.Arg314Trp) (Schuetz_2008) and this individual has subsequently been cited by others (example, Schuetz_2014, Lee_2014, Farmer_2019). The presence of this complex allele representation makes it challenging to capture the impact of this variant in isolation. Therefore, only one report of its presence as a presumed compound heterozygous genotype with p.Arg561Cys in an individual affected with atypical SCID/OS is captured in the context of this evaluation (Villa_2001). These data do not allow any conclusion about variant significance. At least one publication reports experimental evidence evaluating an impact on protein function in isolation (Lee_2014). The most pronounced variant effect results in approximately 16% of normal RAG recombinase activity in-vitro. In another study, the paternally derived complex allele is reported as having 0.09 or 3% of WT activity while the maternal p.Arg314Trp allele had an activity of 0.96 or 30% of WT (Schuetz_2008) in-vitro. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as likely pathogenic citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 507 of the RAG1 protein (p.Arg507Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of severe combined immunodeficiency and Omenn syndrome (PMID: 11133745, 18463379, 28769923). ClinVar contains an entry for this variant (Variation ID: 242791). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on RAG1 protein function. Experimental studies have shown that this missense change affects RAG1 function (PMID: 24290284). 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.