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Cernunnos deficiency is a rare genetic disorder characterized by immunodeficiency, microcephaly, growth retardation, bird-like facies, sensitivity to ionizing radiation, few autoimmune manifestations, premature aging of hematopoietic stem cells at an early age, and occasional myeloproliferative disease. Herein we present five Egyptian Cernunnos patients from 3 different families. We describe the patients' clinical phenotypes, their immunological profile as well as genetic results. Sequence analysis revealed three different mutations in the NHEJ1 gene: a nonsense variant c.532C > T; p.(Arg178Ter), an intronic variant c.178-1G > A and a frameshift insertion variant c.233dup; p.(Asn78LysfsTer14). In conclusion, Cernunnos deficiency can have a wide range of clinical features. The characteristic immune profile including a decrease in recent thymic emigrants and naive T cells, markedly elevated memory T cells together with normal to high IgM, and a decrease in IgG and IgA. This immune profile is highly suggestive of Cernunnos deficiency in T-B-NK + SCID patients especially surviving for older ages. • This is the first Egyptian report of patients with mutations in NHEJ1 gene. • c.532C > T; p.(Arg178Ter), c.178-1G > A and c.233dup had been identified in NHEJ1 gene. • Cernunnos deficiency can have a wide range of clinical features. • Suspicion is raised in SCID with elevated memory and decrease naïve T cells. • Presence of BM aplasia and absence of malignancies are disease hallmarks. [ABSTRACT FROM AUTHOR]