Such complex behaviour is mainly attributed to multiple genes, environmental and cultural factors, but researchers claim that this gene may be responsible for female-to-male transsexuality.
The researchers found that the variation occurs in the gene for an enzyme called cytochrome P17, which is involved in the metabolism of sex hormones.
The presence of this variant causes higher than average tissue concentrations of male and female sex hormones, which in turn affects early brain development.
The variant was discovered by a team led by Clemens Tempfer, after they examined samples from 49 female-to-male (FtM) and 102 male-to-female (MtF) transsexuals, as well as 1669 non-transsexual controls.
The variant was found to be more common in men than women. However, it doesn't seem to be implicated in male-to-female transsexuality (MtF) as the proportion of MtF transsexuals with it was similar to that in non-transsexual men.
However, in women they did encounter were some differences: 44 percent of FtM transsexuals carried it, as against 31 percent of non-transsexual women.
Though there are many women with the variant who are not transsexual and many FtM transsexuals who lack it, the results indicate that the variant makes women more likely to feel that their bodies are of the wrong sex. The findings also raise the possibility that this is a result of their brains having been exposed to higher than average levels of sex hormones during development.
"It may increase the likelihood that people will become transsexual," New Scientist quoted Tempfer, as saying.
However, he also stressed that their cultural environment also plays an important role.
"The present study found that a mutant gene that ultimately results in higher testosterone levels is overrepresented in female-to male transsexualism.
This is in line with what we previously know about masculinisation of the brain and is therefore less likely to be a chance finding.
Hence, the study is important and adds to the notion that gender identity is influenced by sex hormones early in life, and that certain gene combinations make individuals more vulnerable to aberrant effects," said Mikael Landén of the Karolinska Institute in Stockholm, Sweden.
However, Janett Scott, former president of the Beaumont Society, a UK support group for transgender people, has raised concerns that linking transsexuality with biology may encourage people to try and cure it.
"Nature may have made us the way that we are, but nurture is what gives us a problem," she said.
However, Tempfer strongly denied any such motive for his research, saying: "That is completely out of the question," he says.
Nevertheless, he said that if other gene variants with a stronger association to transsexuality are identified, it can be easy to establish a diagnosis. This might allow gender reassignment surgery or hormone therapy to start earlier in life.