Herein, we provide an update on evidence, indication and modalities of alloHSCT for Treg defects (IPEX, CD25-, CTLA-4-, LRBA-, BACH2-deficiency, and STAT3 GOF); autoimmunity disorders (APECED, ITCH-, ZAP70-, TPP2-, JAK1 GOF, and Prolidase deficiency) and immune dysregulation with colitis (IL-10-, IL10Ra-, IL10Rb, and NFAT 5 deficiency) based on data from available literature via PubMed search. This evidence concerns the gene JAK1 and autoimmune disease.