The cause of Goldenhar syndrome is largely unknown. However, it is thought to be multifactorial, although there may be a genetic component, which would account for certain familial patterns. It has been suggested that there is a branchial arch development issue late in the first trimester.

An increase in Goldenhar syndrome in the children of Gulf War veterans has been suggested, but the difference was shown to be statistically insignificant.

Prevalence ranges from 1 in 3500 to 5600 live births. Male-female ratio is found to be 3:2.

Ramos-Arroyo syndrome is marked by corneal anesthesia, absence of the peripapillary choriocapillaris and retinal pigment epithelium, bilateral sensorineural hearing loss, unusual facial appearance, persistent ductus arteriosus, Hirschsprung disease, and moderate intellectual disability. It appears to be a distinct autosomal dominant syndrome with variable expressivity.

As of 2008 this syndrome has only been reported in five individuals within three generations of the same family; two young children, their mother, their uncle and their maternal grandmother. This most recent generation to be diagnosed with Ramos-Arroyo syndrome supports the hypothesis that this disease is a distinct autosomal

dominant disorder. If this syndrome could be identified in other families it may help to discriminate the gene responsible.

Congenital hereditary corneal dystrophy (CHED) is a form of corneal dystrophy which presents at birth.

In a newborn boy thought to have Fryns syndrome, Clark and Fenner-Gonzales (1989) found mosaicism for a tandem duplication of 1q24-q31.2. They suggested that the gene for this disorder is located in that region. However, de Jong et al. (1989), Krassikoff and Sekhon (1990), and Dean et al. (1991) found possible Fryns syndrome associated with anomalies of chromosome 15, chromosome 6, chromosome 8(human)and chromosome 22, respectively. Thus, these cases may all represent mimics of the mendelian syndrome and have no significance as to the location of the gene for the recessive disorder.

By array CGH, Slavotinek et al. (2005) screened patients with DIH and additional phenotypic anomalies consistent with Fryns syndrome for cryptic chromosomal aberrations. They identified submicroscopic chromosome deletions in 3 probands who had previously been diagnosed with Fryns syndrome and had normal karyotyping with G-banded chromosome analysis. Two female infants were found to have microdeletions involving 15q26.2 (see 142340), and 1 male infant had a deletion in band 8p23.1 (see 222400).

Keratitis–ichthyosis–deafness syndrome (also known as "Erythrokeratodermia progressiva Burns," "Ichthyosiform erythroderma, corneal involvement, and deafness," and "KID syndrome,") presents at birth/infancy and is characterized by pregressive corneal opacification, either mild generalized hyperkeratosis or discrete erythematous plaques, and neurosensory deafness.

It is caused by a mutation in connexin 26.

CHED has two types:

- type I or the autosomal dominant form.

- type II or the autosomal recessive form is linked to mutations in SLC4A11 gene

Lisch epithelial corneal dystrophy (LECD), also known as band-shaped and whorled microcystic dystrophy of the corneal epithelium, is a rare form of corneal dystrophy first described in 1992 by Lisch et al. In one study it was linked to chromosomal region Xp22.3, with as yet unknown candidate genes.

The main features of this disease are bilateral or unilateral gray band-shaped and feathery opacities. They sometimes take on a form of a whirlpool, repeating the known pattern of corneal epithelium renewal. Abrasion of the epithelium in 3 patients brought only temporary relief, with abnormal epithelium regrowth in several months.

Epithelial cells in the zones of opacity were shown to have diffuse cytoplasmic vacuoles with as yet unestablished content.

Anterior segment mesenchymal dysgenesis is a failure of the normal development of the tissues of the anterior segment of the eye. It leads to anomalies in the structure of the mature anterior segment, associated with an increased risk of glaucoma and corneal opacity.

Peters' (frequently misspelled Peter's) anomaly is a specific type of mesenchymal anterior segment dysgenesis, in which there is central corneal leukoma, adhesions of the iris and cornea, and abnormalities of the posterior corneal stroma, Descemet's membrane, corneal endothelium, lens, and anterior chamber.

Corneal-cerebellar syndrome (also known as Der Kaloustian-Jarudi-Khoury syndrome) is an autosomally resessive disease that was first described in 1985. Three cases are known: all are sisters in the same family.

Some cases of it are linked to chromosome 10q24, others stem from a mutation in the TGFBI gene.

X-linked endothelial corneal dystrophy (XECD) is a rare form of corneal dystrophy described first in 2006, based on a 4-generation family of 60 members with 9 affected males and 35 trait carriers, which led to mapping the XECD locus to Xq25. It manifests as severe corneal opacification or clouding, sometimes congenital, in the form of a ground glass, milky corneal tissue, and moon crater-like changes of corneal endothelium. Trait carriers manifest only endothelial alterations resembling moon craters.

As of December 2014, the molecular basis for this disease remained unknown, although 181 genes were known to be within the XECD locus, of which 68 were known to be protein-coding.

In France, Aymé, "et al." (1989) estimated the prevalence of Fryns syndrome to be 0.7 per 10,000 births based on the diagnosis of 6 cases in a series of 112,276 consecutive births (live births and perinatal deaths).

It was concluded by Mousa-Al et al. that the disease is different from a disease known as spastic ataxia-corneal dystrophy syndrome that had been found a year later in 1986 in an inbred Bedouin family. Corneal-cerebellar syndrome differs from the spastic ataxia-corneal dystrophy syndrome by causing mental retardation. Corneal dystrophy is also epithelian instead of being stromal.

Thiel–Behnke dystrophy, or Corneal dystrophy of Bowman layer, type II, is a rare form of corneal dystrophy affecting the layer that supports corneal epithelium.

The dystrophy was first described in 1967 and initially suspected to denote the same entity as the earlier-described Reis-Bucklers dystrophy, but following a study in 1995 by Kuchle et al. the two look-alike dystrophies were deemed separate disorders.

Subepithelial mucinous corneal dystrophy (SMCD) is a rare form of corneal dystrophy. It was first described in 1993 by Feder et al. Anterior to Bowman layer, deposits of glycosaminoglycan were detected and identified as chondroitin-4-sulfate and dermatan sulfate.

Several gene mutations have been identified underlying these anomalies with the majority of ASD genes encoding transcriptional regulators. In this review, the role of the ASD genes, PITX2 and FOXC1, is considered in relation to the embryology of the anterior segment, the biochemical function of these proteins, and their role in development and disease aetiology. The emerging view is that these genes act in concert to specify a population of mesenchymal progenitor cells, mainly of neural crest origin, as they migrate anteriorly around the embryonic optic cup. These same genes then regulate mesenchymal cell differentiation to give rise to distinct anterior segment tissues. Development appears critically sensitive to gene dosage, and variation in the normal level of transcription factor activity causes a range of anterior segment anomalies. Interplay between PITX2 and FOXC1 in the development of different anterior segment tissues may partly explain the phenotypic variability and the genetic heterogeneity characteristic of ASD. In the most recent research, the PAX6 gene has been implicated in Peters' Anomaly

Sclerocornea is a congenital anomaly of the eye in which the cornea blends with sclera, having no clear-cut boundary. The extent of the resulting opacity varies from peripheral to total ("sclerocornea totalis"). The severe form is thought to be inherited in an autosomal recessive manner, but there may be another, milder form that is expressed in a dominant fashion. In some cases the patients also have abnormalities beyond the eye (systemic), such as limb deformities and craniofacial and genitourinary defects.

According to one tissue analysis performed after corneal transplantation, the sulfation pattern of keratan sulfate proteoglycans in the affected area is typical for corneal rather than scleral tissue.

Sclerocornea may be concurrent with cornea plana.

The incidence and prevalence of PMD are unknown, and no studies have yet investigated its prevalence or incidence. However, it is generally agreed that PMD is a very rare condition. Some uncertainty regarding the incidence of PMD may be attributed to its confusion with keratoconus. PMD is not linked to race or age, although most cases present early in life, between 20 and 40 years of age. While PMD is usually considered to affect men and women equally, some studies suggest that it may affect men more frequently.

Several diseases have been observed in patients with PMD. However, no causal relationships have been established between any of the associated diseases and the pathogenesis of PMD. Such diseases include: chronic open-angle glaucoma, retinitis pigmentosa, retinal lattice degeneration, scleroderma, kerato-conjunctivitis, eczema, and hyperthyroidism.

In the United States, the incidence of primary congenital glaucoma is about one in 10,000 live births. Worldwide, the incidence ranges from a low of 1:22,000 in Northern Ireland to a high of 1:2,500 in Saudi Arabia and 1:1,250 in Romania. In about two-thirds of cases, it is bilateral. The distribution between males and females varies with geography. In North America and Europe it is more common in boys, whereas in Japan it is more common in girls.

- Congenital glaucoma

- Incidence: one in every 10000-15000 live births.

- Bilateral in up to 80% of cases.

- Most cases are sporadic (90%). However, in the remaining 10% there appears to be a strong familial component.

Macular corneal dystrophy, also known as Fehr corneal dystrophy named for German ophthalmologist Oskar Fehr (1871-1959), is a rare pathological condition affecting the stroma of cornea. The first signs are usually noticed in the first decade of life, and progress afterwards, with opacities developing in the cornea and attacks of pain. The condition was first described by Arthur Groenouw in 1890.

Posterior amorphous corneal dystrophy (PACD) is a rare form of corneal dystrophy. It is not yet linked to any chromosomal locus. The first report describing this dystrophy dates back to 1977.

NF II is a microdeletion syndrome involving mutations in the NF2 gene located at 22q12.2 of chromosome 22. It is an inheritable disorder with an autosomal dominant mode of transmission. Incidence of the condition is about 1 in 60,000. There is a broad clinical spectrum known, but all patients checked have been found to have some mutation of the same gene on chromosome 22. Through statistics, it is suspected that one-half of cases are inherited, and one-half are the result of new, "de novo" mutations.

Familial dysautonomia is seen almost exclusively in Ashkenazi Jews and is inherited in an autosomal recessive fashion. Both parents must be carriers in order for a child to be affected. The carrier frequency in Jewish individuals of Eastern European (Ashkenazi) ancestry is about 1/30, while the carrier frequency in non-Jewish individuals is unknown. If both parents are carriers, there is a one in four, or 25%, chance with each pregnancy for an affected child. Genetic counseling and genetic testing is recommended for families who may be carriers of familial dysautonomia.

Worldwide, there have been approximately 600 diagnoses recorded since discovery of the disease, with approximately 350 of them still living.

Terrien marginal degeneration is a noninflammatory, unilateral or asymmetrically bilateral, slowly progressive thinning of the peripheral corneal stroma.

The cause of Terrien marginal degeneration is unknown, its prevalence is roughly equal between males and females, and it usually occurs in the second or third decade of life.