CRISPR-mediated functional mapping of IL2RG variants in primary human T cells predicts X-linked severe combined immunodeficiency

Distinguishing pathogenic from benign mutation is critical for genetic diagnosis. A CRISPR-targeted saturation genome editing (SGE) platform in primary human cells assessed 489 single nucleotide variants (SNVs) in exon 5 of IL2RG, the gene causing X-linked SCID. The functional impact was clearly defined for 470 variants, agreeing with 100% (18/18) of ClinVar-deposited benign or likely benign annotations, and 100% (42/42) of pathogenic or likely pathogenic annotations. We discovered 90 novel loss-of-function mutations and validated an expected block in T-lymphocyte differentiation from edited hematopoietic stem cells.