Colobomas of the iris may be treated in a number of ways. A simple cosmetic solution is a specialized cosmetic contact lens with an artificial pupil aperture. Surgical repair of the iris defect is also possible. Surgeons can close the defect by stitching in some cases. More recently artificial iris prosthetic devices such as the Human Optics artificial iris have been used successfully by specialist surgeons. This device cannot be used if the natural lens is in place and is not suitable for children. Suture repair is a better option where the lens is still present.

Vision can be improved with glasses, contact lenses or even laser eye surgery but may be limited if the retina is affected or there is amblyopia.

The number of cases is around 0.5 to 0.7 per 10,000 births, making it a relatively rare condition.

Controversies exist around eliminating this disorder from breeding Collies. Some veterinarians advocate only breeding dogs with no evidence of disease, but this would eliminate a large portion of potential breeding stock. Because of this, others recommend only breeding mildly affected dogs, but this would never completely eradicate the condition. Also, mild cases of choroidal hypoplasia may become pigmented and therefore undiagnosable by the age of three to seven months. If puppies are not checked for CEA before this happens, they may be mistaken for normal and bred as such. Checking for CEA by seven weeks of age can eliminate this possibility. Diagnosis is also difficult in dogs with coats of dilute color because lack of pigment in the choroid of these animals can be confused with choroidal hypoplasia. Also, because of the lack of choroidal pigment, mild choroidal hypoplasia is difficult to see, and therefore cases of CEA may be missed.

Until recently, the only way to know if a dog was a carrier was for it to produce an affected puppy. However, a genetic test for CEA became available at the beginning of 2005, developed by the Baker Institute for Animal Health, Cornell University, and administered through OptiGen. The test can determine whether a dog is affected, a carrier, or clear, and is therefore a useful tool in determining a particular dog's suitability for breeding.

It is known to occur in Scotch Collies (smooth and rough collies), Shetland Sheepdogs, Australian Shepherds, Border Collies, Lancashire Heelers, and Nova Scotia Duck Tolling Retrievers. Frequency is high in Collies and Shetland Sheepdogs, and low in Border Collies and NSDTRs. In the United States, incidence in the genotype of collies has been estimated to be as high as 95 percent, with a phenotypic incidence of 80 to 85 percent.

Coloboma of optic nerve, is a rare defect of the optic nerve that causes moderate to severe visual field defects.

Coloboma of the optic nerve is a congenital anomaly of the optic disc in which there is a defect of the inferior aspect of the optic nerve. The issue stems from incomplete closure of the embryonic fissure while in utero. A varying amount of glial tissue typically fills the defect, manifests as a white mass.

Photophobia may also affect patients' socioeconomic status by limiting their career choices, since many workplaces require bright lights for safety or to accommodate the work being done. Sufferers may be shut out of a wide range of both skilled and unskilled jobs, such as in warehouses, offices, workshops, classrooms, supermarkets and storage spaces. Some photophobes are only able to work night shifts, which reduces their prospects for finding work.

The best treatment for light sensitivity is to address the underlying cause. Once the triggering factor is treated, photophobia disappears in many but not all cases.

People with photophobia will avert their eyes from direct light, such as sunlight and room lights. They may seek the shelter of a dark room. They may wear sunglasses designed to filter peripheral light and wide-brimmed sun hats.

Wearing sunglasses indoors can make symptoms worse over time as it will dark-adapt the retina which aggravates sensitivity to light. Indoor photophobia symptoms may be relieved with the use of precision tinted lenses which block the green-to-blue end of the light spectrum without blurring or impeding vision.

A paper by Stringham and Hammond, published in the "Journal of Food Science", reviews studies of effects of consuming Lutein and Zeaxanthin on visual performance, and notes a decrease in sensitivity to glare.

People with hemeralopia may benefit from sunglasses. Wherever possible, environmental illumination should be adjusted to comfortable level. Light-filtering lenses appear to help in people reporting photophobia.

Otherwise, treatment relies on identifying and treating any underlying disorder.

Although both optic nerve colobomas and morning glory disc anomaly (MGDA) involve mutations of the PAX6 gene, these two separate diseases represent two distinct causes. An optic nerve coloboma is easily differentiated from morning glory anomaly. Colobomas affect only the inferior aspect of the nerve as it represents an incomplete closure of the embryonic fissure, whereas MGDA encompasses all aspects of the nerve and represents more generally a dysgenesis of the mesoderm.

Lenz microphthalmia syndrome (or LMS) is a very rare inherited disorder characterized by abnormal smallness of one or both eyes (microphthalmos) sometimes with droopy eyelids (blepharoptosis), resulting in visual impairment or blindness. Eye problems may include coloboma, microcornea, and glaucoma. Some affected infants may have complete absence of the eyes (anophthalmia). Most affected infants have developmental delay and intellectual disability, ranging from mild to severe. Other physical abnormalities associated with this disorder can include an unusually small head (microcephaly), and malformations of the teeth, ears, fingers or toes, skeleton, and genitourinary system. The range and severity of findings vary from case to case. Formal diagnosis criteria do not exist.

Lenz microphthalmia syndrome is inherited as an X-linked recessive genetic trait and is fully expressed in males only. Females who carry one copy of the disease gene (heterozygotes) may exhibit some of the symptoms associated with the disorder, such as an abnormally small head (microcephaly), short stature, or malformations of the fingers or toes. Molecular genetic testing of BCOR (MCOPS2 locus), the only gene known to be associated with Lenz microphthalmia syndrome, is available on a clinical basis. One additional locus on the X chromosome (MCOPS1) is known to be associated with LMS.

Lenz microphthalmia syndrome is also known as LMS, Lenz syndrome, Lenz dysplasia, Lenz dysmorphogenetic syndrome, or microphthalmia with multiple associated anomalies (MAA: OMIM 309800). It is named after Widukind Lenz, a German geneticist and dysmorphologist.

A somewhat similar X-linked syndrome of microphthalmia, called oculofaciocardiodental syndrome (OFCD) is associated with mutations in BCOR. OFCD syndrome is inherited in an X-linked dominant pattern with male lethality.

Papillorenal syndrome, also called renal-coloboma syndrome or isolated renal hypoplasia, is an autosomal dominant genetic disorder marked by underdevelopment (hypoplasia) of the kidney and colobomas of the optic nerve.

Approximately half of patients with papillorenal syndrome do not have defects in the "Pax2". This suggests that other genes play a role in the development of the syndrome, though few downstream effectors of "Pax2" have been identified.

Hemeralopia is known to occur in several ocular conditions. Cone dystrophy and achromatopsia, affecting the cones in the retina, and the anti-epileptic drug Trimethadione are typical causes. Adie's pupil which fails to constrict in response to light; Aniridia, which is absence of the iris; Albinism where the iris is defectively pigmented may also cause this. Central Cataracts, due to the lens clouding, disperses the light before it can reach the retina, is a common cause of hemeralopia and photoaversion in elderly. C.A.R (Cancer Associated Retinopathy) seen when certain cancers incite the production of deleterious antibodies against retinal components, may cause hemeralopia.

Another known cause is a rare genetic condition called Cohen Syndrome (aka Pepper Syndrome). Cohen syndrome is mostly characterized by obesity, mental retardation, and craniofacial dysmorphism due to genetic mutation at locus 8q22-23. Rarely it may have ocular complications such as hemeralopia, pigmentary chorioretinitis, optic atrophy or retinal/iris coloboma, having a serious effect on the person's vision.

Yet another cause of hemeralopia is uni- or bilateral postchiasmatic brain injury. This may also cause concomitant night blindness.

Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

In the movie City of Angels, Dr. Maggie Rice (played by Meg Ryan) correctly diagnoses the cause of a newborn baby's failure to thrive as due to choanal atresia.

Because the cause of facial clefts still is unclear, it is difficult to say what may prevent children being born with facial clefts. It seems that folic acid contributes to lowering the risk of a child being born with a facial cleft.

Congenital cystic eye (also known as "CCE" or "cystic eyeball") is an extremely rare ocular malformation where the eye fails to develop correctly "in utero" and is replaced by benign, fluid-filled tissue. Its incidence is unknown, due to the very small number of cases reported. An audit by Duke-Elder of the medical literature from 1880 to 1963 discovered only 28 cases. The term was coined in 1937 by the renowned ophthalmologist Ida Mann.

Embryologically, the defect is thought to occur around day 35 of gestation, when the vesicle fails to invaginate. Dysgenesis of the vesicle later in development may result in coloboma, a separate and less severe malformation of the ocular structures.

CCE is almost always unilateral, but at least 2 cases of bilateral involvement have been described. Patients may also present with skin appendages attached to the skin surrounding the eyes. Association with intracranial anomalies has been reported.

Treatment of CCE is usually by enucleation, followed by insertion of an ocular implant and prosthesis.

There are several options for treatment of mouth anomalies like Tessier cleft number 2-3-7 . These clefts are also seen in various syndromes like Treacher Collins syndrome and hemifacial microsomia, which makes the treatment much more complicated. In this case, treatment of mouth anomalies is a part of the treatment of the syndrome.

If the diagnostic workup reveals a systemic disease process, directed therapies to treat that underlying cause should be initiated. If the amaurosis fugax is caused by an atherosclerotic lesion, aspirin is indicated, and a carotid endarterectomy considered based on the location and grade of the stenosis. Generally, if the carotid artery is still patent, the greater the stenosis, the greater the indication for endarterectomy. "Amaurosis fugax appears to be a particularly favorable indication for carotid endarterectomy. Left untreated, this event carries a high risk of stroke; after carotid endarterectomy, which has a low operative risk, there is a very low postoperative stroke rate." However, the rate of subsequent stroke after amaurosis is significantly less than after a hemispheric TIA, therefore there remains debate as to the precise indications for which a carotid endarterectomy should be performed. If the full diagnostic workup is completely normal, patient observation is recommended.

The outcome of this disease is dependent on the severity of the cardiac defects. Approximately 1 in 3 children with this diagnosis require shunting for the hydrocephaly that is often a consequence. Some children require extra assistance or therapy for delayed psychomotor and speech development, including hypotonia.

The treatment of individuals with TCS may involve the intervention of professionals from multiple disciplines. The primary concerns are breathing and feeding, as a consequence of the hypoplasia of the mandibula and the obstruction of the hypopharynx by the tongue. Sometimes, they may require a tracheostomy to maintain an adequate airway, and a gastrostomy to assure an adequate caloric intake while protecting the airway. Corrective surgery of the face is performed at defined ages, depending on the developmental state.

An overview of the present guidelines:

- If a cleft palate is present, the repair normally takes place at 9–12 months old. Before surgery, a polysomnography with a palatal plate in place is needed. This may predict the postoperative situation and gives insight on the chance of the presence of sleep apnea (OSAS) after the operation.

- Hearing loss is treated by bone conduction amplification, speech therapy, and educational intervention to avoid language/speech problems. The bone-anchored hearing aid is an alternative for individuals with ear anomalies

- Zygomatic and orbital reconstruction is performed when the cranio-orbitozygomatic bone is completely developed, usually at the age of 5–7 years. In children, an autologous bone graft is mostly used. In combination with this transplantation, lipofilling can be used in the periorbital area to get an optimal result of the reconstruction. Reconstruction of the lower eyelid coloboma includes the use of a myocutaneous flap, which is elevated and in this manner closes the eyelid defect.

- External ear reconstruction is usually done when the individual is at least eight years old. Sometimes, the external auditory canal or middle ear can also be treated.

- The optimal age for the maxillomandibular reconstruction is controversial; as of 2004, this classification has been used:

1. Type I (mild) and Type IIa (moderate) 13–16 years

2. Type IIb (moderate to severe malformation) at skeletal maturity

3. Type III (severe) 6–10 years

- When the teeth are cutting, the teeth should be under supervision of an orthodontist to make sure no abnormalities occur. If abnormalities like dislocation or an overgrowth of teeth are seen, appropriate action can be undertaken as soon as possible.

- Orthognatic treatments usually take place after the age of 16 years; at this point, all teeth are in place and the jaw and dentures are mature. Whenever OSAS is detected, the level of obstruction is determined through endoscopy of the upper airways. Mandibular advancement can be an effective way to improve both breathing and æsthetics, while a chinplasty only restores the profile.

- If a nose reconstruction is necessary, it is usually performed after the orthognatic surgery and after the age of 18 years.

- The contour of the facial soft tissues generally requires correction at a later age, because of the facial skeletal maturity. The use of microsurgical methods, like the free flap transfer, has improved the correction of facial soft tissue contours. Another technique to improve the facial soft tissue contours is lipofilling. For instance, lipofilling is used to reconstruct the eyelids.

The disorder can be associated with a number of psychological symptoms, anxiety, depression, social phobia, body image disorders, and patients may be subjected to discrimination, bullying and name calling especially when young. A multi-disciplinary team and parental support should include these issues.

Prognoses for 3C syndrome vary widely based on the specific constellation of symptoms seen in an individual. Typically, the gravity of the prognosis correlates with the severity of the cardiac abnormalities. For children with less severe cardiac abnormalities, the developmental prognosis depends on the cerebellar abnormalities that are present. Severe cerebellar hypoplasia is associated with growth and speech delays, as well as hypotonia and general growth deficiencies.

CHARGE syndrome (formerly known as CHARGE association), is a rare syndrome caused by a genetic disorder. First described in 1979, the acronym "CHARGE" came into use for newborn children with the congenital features of coloboma of the eye, heart defects, atresia of the nasal choanae, retardation of growth and/or development, genital and/or urinary abnormalities, and ear abnormalities and deafness. These features are no longer used in making a diagnosis of CHARGE syndrome, but the name remains. About two thirds of cases are due to a CHD7 mutation. CHARGE syndrome occurs only in 0.1–1.2 per 10,000 live births; as of 2009 it was the leading cause of congenital deafblindness in the US.

Yim–Ebbin syndrome is a congenital disorder characterized by the absence of arms, a cleft lip and palate, hydrocephalus, and an iris coloboma. It was first described by Yim and Ebbin in 1982, and later by Thomas and Donnai in 1994. In 1996, a third case was reported by Froster et al. who suggested that the three cases were related and represented a distinct syndrome. In 2000, a similar case was reported by Pierri et al.

It is also known as "amelia cleft lip palate hydrocephalus iris coloboma".