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Background  Polymorphisms in the vitamin K-epoxide reductase complex subunit 1 gene,  Vkorc1 , could affect blood coagulation and other vitamin K-dependent proteins, such as osteocalcin (bone Gla protein, BGP). Here we sequenced the  Vkorc1  gene in 40 mouse priority strains. We analyzed  Vkorc1  haplotypes with respect to prothrombin time (PT) and bone mineral density and composition (BMD and BMC); phenotypes expected to be vitamin K-dependent and represented by data in the Mouse Phenome Database (MPD).    Findings  In the commonly used laboratory strains of  Mus musculus domesticus  we identified only four haplotypes differing in the intron or 5' region sequence of the  Vkorc1 . Six haplotypes differing by coding and non-coding polymorphisms were identified in the other subspecies of  Mus . We detected no significant association of  Vkorc1  haplotypes with PT, BMD and BMC within each subspecies of  Mus .  Vkorc1  haplotype sequences divergence between subspecies was associated with PT, BMD and BMC.    Conclusion  Phenotypic variation in PT, BMD and BMC within subspecies of  Mus , while substantial, appears to be dominated by genetic variation in genes other than the  Vkorc1 . This was particularly evident for  M. m. domesticus , where a single haplotype was observed in conjunction with virtually the entire range of PT, BMD and BMC values of all 5 subspecies of  Mus  included in this study. Differences in these phenotypes between subspecies also should not be attributed to  Vkorc1  variants, but should be viewed as a result of genome wide genetic divergence.

Vitamin K epoxide reductase complex subunit 1 (Vkorc1) haplotype diversity in mouse priority strains