The NM_000536.4:c.829dup variant in RAG2 is a frameshift variant predicted to result in a truncated protein (p.Tyr277Leufs*4). Although this variant is expected to escape nonsense-mediated decay (NMD), it would be expected to disrupt approximately 47% of the RAG2 protein. In addition, this variant would be expected to disrupt/remove the entire PHD domain (amino acids 414-487), which is defined as a mutational hotspot/critical functional domain by the ClinGen SCID VCEP (PMID: 15964836). PVS1 met. This variant is absent in gnomAD, which is below the threshold for max filtering allele frequency for PM2_Supporting set by the ClinGen SCID VCEP for RAG2 (<0.0000588). In an experimental study, this variant demonstrates zero recombination activity, which is below the threshold outlined by the ClinGen SCID VCEP (< 25% wildtype activity) for PS3_Moderate (PMID: 31058115). This variant has been reported in three patients. One patient in a cohort of SCID patients (0.5p) with T-B-NK+ immunophenotype (0.5p) was identified with this variant along with a co-occurring RAG2 p.Phe183Asn variant, though phase was not reported (PMID: 24144642) (1p, PP4). A second patient with a later onset CID-like phenotype was identified with this variant along with a co-occurring RAG2 p.Glu170Gly variant (only one parent tested and was heterozygous for the variant) (PMID: 31058115). The p.Phe183Asn and p.Glu170Gly variants have not yet been classified by the ClinGen SCID VCEP. A third patient with Omenn syndrome was identified with this variant; however, the variant was heterozygous, and a second variant in RAG2 was not identified (PMID: 34851571). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive SCID based on the ACMG criteria applied: PVS1, PM2_Supporting, PS3_Moderate, and PP4 as specified by the ClinGen SCID VCEP (VCEP specifications version 1).