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The lectin pathway of the complement system is activated when mannan-binding lectin (MBL) in complex with MBL-associated serine protease 2 (MASP-2) binds to carbohydrate structures on microorganisms. Structural gene mutations and promoter polymorphisms in the MBL2 gene responsible for low-MBL serum levels are present in all human populations and associate with increased risk of infection. Recently, investigations on Danes revealed the existence of a mutation on the MASP2 gene, which introduces an amino acid substitution in the CUB1 domain (Asp105Gly; numbering refers to the mature protein), and is associated with reduction in the level of MASP-2 in serum. Here, we present the results of a sequence-based typing analysis of the MBL2 and MASP2 gene polymorphisms in a group of 65 Africans (50 North Africans and 15 Sub-Saharan) and of 104 Spaniards. The analysis identified three novel exon 3 MASP2 variants introducing amino acid substitutions at positions 84 (Arg-->Gln), 103 (Arg-->Cys) and 111 (Pro-->Leu) in the CUB1 domain. None of these variants were identified in Spaniards. The Arg84Gln was detected in four of the 15 Sub-Saharans. The Arg103Cys and Pro111Leu variants were detected only among North Africans (two and four individuals, respectively). The Asp105Gly variant was similarly represented among Spaniards and North Africans (three and two individuals, respectively), which appears to be a lower frequency than that reported for Danes (5.5%). As reported for MBL2, the marked geographic distribution of the new MASP2 variants may represent an evolutionary adaptation to different environments.