Aberrant splicing caused by a homozygous AK2 c.498 + 1G > A variant in a patient with reticular dysgenesis and concurrent B-cell acute lymphoblastic leukemia

Abstract

Reticular dysgenesis (RD) is a rare autosomal recessive severe combined immunodeficiency characterized by profound neutropenia, T-cell lymphopenia and sensorineural hearing loss, and is caused by biallelic loss-of-function variants in AK2. We identified a homozygous AK2 splice-site variant (c.498 + 1G > A) in a boy with RD and concurrent B-cell acute lymphoblastic leukemia (B-ALL), a clinical combination not previously reported in association with an AK2 variant. An in vitro minigene assay showed that c.498 + 1G > A disrupts the canonical 5′ splice donor site and generates an aberrant transcript carrying a 4-bp intronic insertion after exon 5, which causes a frameshift and introduces a premature termination codon; the transcript is predicted to be degraded by nonsense-mediated mRNA decay or, if translated, to yield a non-functional truncated protein, leading to loss of AK2 function. The variant was classified as pathogenic according to the ACMG/AMP criteria. As patient-derived material was unavailable, we re-analyzed publicly available RNA-seq data from AK2-knockout human hematopoietic stem and progenitor cells (GSE179320) and identified six hub genes (APOE, TREM2, CD68, CD36, IRF8 and CD163), which we further validated at the mRNA level in AK2-knockdown HL-60 cells, with IRF8 showing the most pronounced upregulation. This study characterizes the splicing defect caused by this variant and identifies candidate AK2-associated genes; the coexistence of RD and B-ALL is reported as a clinical observation requiring further investigation.