This clincal report presents the case of a six-month-old male infant with suspected left testicular torsion and right cryptorchidism, who exhibited prolonged activated partial thromboplastin time (aPTT) and prothrombin time (PT), microcytic anemia, and elevated plasma levels of aspartate aminotransferase (AST). Physical examination revealed pale skin and small subcutaneous hematomas, but no significant signs of cholestasis or other abnormalities. The family history included unspecified coagulation disorders. After treating the anemia with iron supplements, repeated coagulation tests confirmed deficiencies in multiple coagulation factors, with normal or elevated FVIII levels. Major genetic and autoimmune causes were initially ruled out, and other potential conditions, such as vitamin K deficiency and liver disease, were considered but not confirmed. At age six, the patient was hospitalized again due to macrohematuria. Further testing showed persistent coagulation abnormalities and elevated AST levels. Whole-exome sequencing identified a de novo heterozygous variant in the SLC37A4 gene, associated with glycosylation disorders and liver dysfunction. Additionally, congenital malformation of the C1 vertebra was discovered. Glycosylation analysis of transferrin revealed a marked alteration, supporting the involvement of the SLC37A4 variant in the patient’s condition. This case highlights the importance of considering glycosylation disorders in patients presenting with coagulopathy, liver dysfunction, and skeletal abnormalities. It also emphasizes the role of genetic testing in diagnosing rare disorders and the potential implications of glycosylation in the regulation of coagulation factor activity.