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Identification and structural analysis of a novel FUT1 c.789C>A variant and previously reported para-Bombay alleles
Sunitha Vege1, William Crews2, June Fuertes1
1Immunohematology and Genomics Laboratory, New York Blood Center, New York, New York, USA.
Background:
FUT1 encodes galactoside alpha-(1,2)-fucosyltransferase 1 (α2FucT1), which adds the H antigen glycan on red blood cells. In contrast, FUT2 encodes galactoside alpha-(1,2)-fucosyltransferase 2 (α2FucT2), which is primarily responsible for adding H antigen in secretions. When FUT1 loss-of-function variants occur in the presence of functional FUT2, RBCs can exhibit on their surface weak H antigen captured from secretions. This is known as the para-Bombay phenotype.
Study Design And Methods:
Whole genome sequencing (WGS) was conducted on a sample from a Hispanic individual exhibiting the para-Bombay phenotype. The analysis focused on FUT1, FUT2, and ABO. To assess potential loss-of-function missense variants in FUT1, a three-dimensional structural model of human α2FucT1 complexed with its donor substrate GDP-L-Fucose and its acceptor glycan Galβ1-4GlcNAc was generated using AlphaFold2 and refined through molecular docking.
Results:
Whole genome sequencing revealed that the para-Bombay individual was homozygous for a rare FUT1 missense variant (c.789C>A, p.Asn263Lys). Structural modeling demonstrated that this substitution lies near the GDP-L-Fucose binding site in the donor glycan pocket, leading to a predicted alteration in electrostatic charge distribution. Moreover, analysis of previously published loss-of-function missense FUT1 variants, specifically p.Met228Ile, p.Trp232Arg, p.Ser262Lys, and p.Asn263His, revealed similar charge shifts near the donor or acceptor glycan binding sites within the enzyme's catalytic center, suggesting a common loss-of-function mechanism.
Conclusion:
This study identified a novel FUT1 variant associated with the para-Bombay phenotype and elucidated its structural impact on α2FucT1 function using an AlphaFold2-based structural model.
