Also the child is born with fingers and toes that are fused together along with abnormalities within the urine tract. As this disorder relates to vaginal atresia, infants born with Fraser syndrome are also born with malformations in their genitals. McKusick-Kaufman syndrome
A female with McKusick-Kaufman syndrome has vaginal atresia that is often present with imperforate anus, heart defects, hydrometrocolpos, and/or polydactyly,  The female will still develop secondary sexual characteristics. Mechanism
The exact mechanism for vaginal atresia is not well known, as specific molecular mechanisms which lead to the closing or absence of the vagina are unclear. There are various pathways that may support or restrict regular vaginal development. Research has shown that changing factors may also include paracrine and autocrine signals and changes in the basis of developing organs. Specific patterns of genetic transmission have not been identified for this condition. Normal reproductive organ production requires timely coordination of the following systems: external genitalia, internal ductal system, and gonadal structure. The abnormal development of the vagina results in an incomplete unit (low, mid, high transverse septum), failure of epithelium degeneration (imperforate hymen), and vaginal atresia.According to a number of medical professionals, timely coordination of interdependent systems is required for normal reproductive organ development in both males and females. The description of vaginal atresia mechanism can be explained in several steps of development of the uterovaginal canal per the information provided by these medical professionals. These interdependent systems are external genitalia, gonadal structures, and internal ductal system.
Typically, one of these ducts develops in the fallopian tubes while the other ducts develop into the vagina and uterus. Vaginal atresia is found to occur when the urogenital sinus does not contribute to the formation of the lower portion of the vagina. As previously mentioned, there are other disorders or syndromes that are found in conjunction with individuals living with vaginal atresia. These disorders are:

Rokitansky-Mayer-Küster-Hauser syndrome
Rokitansky-Mayer-Küster-Hauser syndrome is a disorder in females that causes the uterus and vagina to be absent or underdeveloped. Those born with this disorder are considered to be genetic female and have a 46XX chromosomes. Kidney anomalies often accompany this disorder as well. Also referred to as Müllerian agenesis, vaginal agenesis, or Müllerian aplasia, this disorder affects 1 in every 4,000-5,000 females. A cloacal malformation often accompanies this disorder, which is the surgical treatment that incorporates several vaginal replacement techniques. This disorder is caused by an implication in the WNT4 protein coding gene, which is found on the short arm (p) of chromosome 1. A genetic mutation occurs causing a substitution of leucine to proline residue at position 12 on the amino acid in the WNT4 protein. Essentially, this will cause a reduction in the intranuclear levels of β catenin. Additionally, steroidogenic enzymes such as 17α-hydroxylase and 3β-hydroxysteriod dehydrogenase are inhibited because of this mutation, which leads to an excess amount to androgen in the system.