Introduction: Severe Congenital Neutropenia Type 4, is a rare autosomal recessive disorder caused by G6PC3 deficiency . We report a 5-year-old boy presenting with clinical features consistent with SCN4 in whom a novel homozygous missense variant in the G6PC3 gene was dentified. This case emphasizes the importance of detailed phenotypic analysis in evaluating novel genetic variants and expands the known genotypic spectrum of SCN4. Case presentation: A 5-year-old boy , the third child of healthy non-consanguineous parents, presented with recurrent infections since infancy , including urinary tract, respiratory , parotid abscess and sepsis. He was born at term (3.1kg) with neonatal complications involving meconium aspiration syndrome and secondary sepsis. Moderate to severe neutropenia was identified at 2 months and has persisted since. Immunological evaluation revealed decreased T-cell subsets (CD19, CD4, CD8) despite normal immunoglobulins. Extra-hematological manifestations included prognathism, flat nasal bridge, low hairline, distended superficial veins on the lower limbs, atrial septal defect, cylindrical bronchiectasis, bilateral inguinal hernia, leftsided undescended testis, small joint arthritis, failure to thrive, and chronic diarrhoea. Molecular testing identified a novel homozygous missense variant in the G6PC3 gene. Treatment with Empagliflozin was initiated with successful outcome. Conclusion: This case reports a novel G6PC3 missense variant in a patient with clinical and laboratory features strongly consistent with SCN4. It highlights the broad spectrum of clinical manifestations associated with G6PC3 deficiency and emphasizes the importance of considering this diagnosis in patients with congenital neutropenia and multisystem involvement. Furthermore, it suggests the potential of empagliflozin as a treatment approach in this challenging condition.