Objective To define the loci of the mutant gene in the loop-tail mouse.Methods To study the heredity pattern, loop-tail mice were mated with normal C57BL/6J and C3H mice. Their offsprings with loop-tail or normal phenotype were registered respectively. Microsatellite marker D1Mit113 and D1Mit149 were used to locate the mutant gene. Based on fine mapping, the candidate gene Vangl2 was found. Vangl2 gene from the loop-tail mice was amplified by PCR followed by sequencing. Incision enzyme FspBI(BfaI)identified the genotype of offspring from loop-tail mice intercrossing. Results Heredity test indicated that the loop-tail phenotype was controlled by a single dominant gene not with 100% penetrance but was affected by genetic background. A C-to-T transversion was at the 1345bp in Vangl2 gene of the loop-tail mice.Conclusions The C-to-T transversion introduces a pre-termination codon of amino acids and causes the phenotype of loop-tail phenotype. None homozygous mice were found in the offsprings, suggesting that the homozygous mice are lethal.