Amblyopia is diagnosed by identifying low visual acuity in one or both eyes, out of proportion to the structural abnormality of the eye and excluding other visual disorders as causes for the lowered visual acuity. It can be defined as an interocular difference of two lines or more in acuity (e.g. on Snellen chart) when the eye optics is maximally corrected. In young children, visual acuity is difficult to measure and can be estimated by observing the reactions of the patient reacts when one eye is covered, including observing the patient's ability to follow objects with one eye.

Stereotests like the Lang stereotest are not reliable exclusion tests for amblyopia. A person who passes the Lang stereotest test is unlikely to have strabismic amblyopia, but could nonetheless have refractive or deprivational amblyopia. It has been suggested that binocular retinal birefringence scanning may be able to identify, already in very young children, amblyopia that is associated with strabismus, microstrabismus, or reduced fixation accuracy. Diagnosis and treatment of amblyopia as early as possible is necessary to keep the vision loss to a minimum.

Screening for amblyopia is recommended in all people between three and five years of age.

Typically a coloboma appears oval or comet shaped with round end towards the centre. There may be a few vessels (retinal or choroidal) at the edges. The surface may have irregular depression.

During an eye examination, a test such as cover testing or the Hirschberg test is used in the diagnosis and measurement of strabismus and its impact on vision. Retinal birefringence scanning can be used for screening of young children for eye misaligments.

Several classifications are made when diagnosing strabismus.

During an eye examination, the presence of suppression and the size and location of the suppression scotoma may be the Worth 4 dot test (a subjective test that is considered to be the most precise suppression test), or with other subjective tests such as the Bagolini striated lens test, or with objective tests such as the 4 prism base out test.

Between 2 and 5% of the population in western countries have amblyopia. In the U.K., 90% of visual health appointments in the child are concerning amblyopia.

Depending on the chosen criterion for diagnosis, between 1 and 4% of the children have amblyopia.

The diagnosis of Kaufman oculocerebrofacial syndrome can be achieved via molecular testing approaches. Additionally to ascertain if the individual has the condition:

- Growth assessment

- Thyroid function evaluation

- Kidney ultrasound

- Echocardiogram

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 prognosis for each patient with esotropia will depend upon the origin and classification of their condition. However, in general, management will take the following course:

1. Identify and treat any underlying systemic condition.

2. Prescribe any glasses required and allow the patient time to 'settle into' them.

3. Use occlusion to treat any amblyopia present and encourage alternation.

4. Where appropriate, orthoptic exercises can be used to attempt to restore binocularity.

5. Where appropriate, prismatic correction can be used, either temporarily or permanently, to relieve symptoms of double vision.

6. In specific cases, and primarily in adult patients, botulinum toxin can be used either as a permanent therapeutic approach, or as a temporary measure to prevent contracture of muscles prior to surgery

7. Where necessary, extra-ocular muscle surgery can be undertaken to improve cosmesis and, on occasion, restore binocularity.

Kaufman oculocerebrofacial syndrome differential diagnosis consists of:

There is no known cure for this syndrome. Patients usually need ophthalmic surgery and may also need dental surgery

Genetic counseling and screening of the mother's relatives is recommended.

Suppression may treated with vision therapy, though there is a wide range of opinions on long-term effectiveness between eye care professionals, with little scientific evidence of long-term improvement of suppression, if the underlying cause is not addressed (strabismus, amblyopia, etc.).

Strabismus can be manifest ("-tropia") or latent ("-phoria"). A manifest deviation, or heterotropia (which may be "eso-", "exo-", "hyper-", "hypo-", "cyclotropia" or a combination of these), is present while the patient views a target binocularly, with no occlusion of either eye. The patient is unable to align the gaze of each eye to achieve fusion. A latent deviation, or heterophoria ("eso-", "exo-", "hyper-", "hypo-", "cyclophoria" or a combination of these), is only present after binocular vision has been interrupted, typically by covering one eye. This type of patient can typically maintain fusion despite the misalignment that occurs when the positioning system is relaxed. Intermittent strabismus is a combination of both of these types, where the patient can achieve fusion, but occasionally or frequently falters to the point of a manifest deviation.

A clinical diagnosis of SCS can be verified by testing the TWIST1 gene (only gene in which mutations are known to cause SCS) for mutations using DNA analysis, such as sequence analysis, deletion/duplication analysis, and cytogenetics/ FISH analysis. Sequence analysis of exon 1 (TWIST1 coding region) provides a good method for detecting the frequency of mutations in the TWIST1 gene. These mutations include nonsense, missense, splice site mutation, and intragenic deletions/insertions. Deletion/duplication analysis identifies mutations in the TWIST1 gene that are not readily detected by sequence analysis. Common methods include PCR, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray (CMA). Cytogenetic/FISH analysis attaches fluorescently labels DNA markers to a denatured chromosome and is then examined under fluorescent lighting, which reveals mutations caused by translocations or inversions involving 7p21. Occasionally, individuals with SCS have a chromosome translocation, inversion, or ring chromosome 7 involving 7p21 resulting in atypical findings, such as, increased developmental delay. Individuals with SCS, typically have normal brain functioning and rarely have mental impairments. For this reason, if an individual has both SCS and mental retardation, then they should have their TWIST1 gene screened more carefully because this is not a normal trait of SCS. Cytogenetic testing and direct gene testing can also be used to study gene/chromosome defects. Cytogenetic testing is the study of chromosomes to detect gains or losses of chromosomes or chromosome segments using fluorescent in situ hybridization (FISH) and/or comparative genomic hybridization (CGH). Direct gene testing uses blood, hair, skin, amniotic fluid, or other tissues in order to find genetic disorders. Direct gene testing can determine whether an individual has SCS by testing the individual's blood for mutations in the TWIST1 gene.

Incomitant esotropias are conditions in which the esotropia varies in size with direction of gaze. They can occur in both childhood and adulthood, and arise as a result of neurological, mechanical or myogenic problems. These problems may directly affect the extra-ocular muscles themselves, and may also result from conditions affecting the nerve or blood supply to these muscles or the bony orbital structures surrounding them. Examples of conditions giving rise to an esotropia might include a VIth cranial nerve (or Abducens) palsy, Duane's syndrome or orbital injury.

Up until recently, experts frequently disagreed on whether a patient had SCS, Crouzon syndrome, isolated craniosynostosis, or some other disease because the symptoms are so closely related, they literally had no way of differentiating between all of them. However, we now have direct gene testing, which allows for a more definitive diagnosis because it allows them to be differentiated from each other based on which gene is mutated in each condition. The following is a list of conditions commonly confused/misdiagnosed for SCS, some of their symptoms, and which mutated gene each contains:

Brain MRI shows vermis atrophy or hypoplasic. Cerebral and cerebellar atrophy with white matter changes in some cases.

The assessment for Smith-Finemen-Myers syndrome like any other mental retardation includes a detailed family history and physical exam that tests the mentality of the patient. The patient also gets a brain and skeletal imaging though CT scans or x-rays. They also does a chromosome study and certain other genetic biochemical tests to help figure out any other causes for the mental retardation.

The diagnosis of SFMS is based on visible and measurable symptoms. Until 2000, SFMS was not known to be associated with any particular gene. As of 2001, scientists do not yet know if other genes are involved in this rare disease. Generic analysis of the ATRX gene may prove to be helpful in diagnosis of SFMS.

Ametropic amblyopia, is a medical condition in which the retina cannot focus on the image of a distant object, a condition often described as reduced visual acuity. This is due to large uncorrected refractive errors in the patient's optic system of the eyes. Astigmatism is one of the most frequent causes of ametropic amblyopia.

In general, children with a small isolated nevus and a normal physical exam do not need further testing; treatment may include potential surgical removal of the nevus. If syndrome issues are suspected, neurological, ocular, and skeletal exams are important. Laboratory investigations may include serum and urine calcium and phosphate, and possibly liver and renal function tests. The choice of imaging studies depends on the suspected abnormalities and might include skeletal survey, CT scan of the head, MRI, and/or EEG.

Depending on the systems involved, an individual with Schimmelpenning syndrome may need to see an interdisciplinary team of specialists: dermatologist, neurologist, ophthalmologist, orthopedic surgeon, oral surgeon, plastic surgeon, psychologist.

Nance–Horan syndrome is a rare X linked syndrome characterized by congenital cataract leading to profound vision loss, characteristic dysmorphic features and dental anomalies. Microcornea, microphthalmia and mild or moderate mental retardation may accompany these features. Heterozygous females often manifest similarly but with less severe features than affected males.

The diagnosis of Mulibrey nanism can be done via genetic testing, as well as by the physical characteristics (signs/symptoms) displayed by the individual.

X-ray and neuroimaging studies may be helpful in confirming a diagnosis of Coffin–Lowry syndrome. Decreased ribosomal S6 kinase activity in cultured fibroblast or transformed lymphoblast cells from a male indicates Coffin–Lowry syndrome. Studies of enzyme activity can not be used to diagnose an affected female.

Molecular genetic testing on a blood specimen or cells from a cheek swab is available to identify mutations in the RSK2 gene. This testing can be used to confirm but not rule out the diagnosis of Coffin–Lowry syndrome because not all affected individuals have a detectable mutation.

There is currently no cure for GAPO syndrome, but some options are available to reduce the symptoms. Nearsightedness, which affects some sufferers of the disease, can be treated by corrective lenses. Unfortunately, optic atrophy as a result of degradation of the optic nerve (common with GAPO syndrome) cannot be corrected. Corticosteroids have been proposed as a treatment for optic nerve atrophy, but their effectiveness is disputed, and no steroid based treatments are currently available.

Diagnosis of MSS is based on clinical symptoms, magnetic resonance imaging (MRI) of the brain (cerebellar atrophy particularly involving the cerebellar vermis), and muscle biopsy.

It can be associated with mutations of the SIL1 gene, and a mutation can be found in about 50% of cases.

Differential diagnosis includes Congenital Cataracts Facial Dysmorphism Neuropathy (CCFDN), Marinesco–Sjögren like syndrome with chylomicronemia, carbohydrate deficient glycoprotein syndromes, Lowe syndrome, and mitochondrial disease.

Recent research has been focused on studying large series of cases of 3-M syndrome to allow scientists to obtain more information behind the genes involved in the development of this disorder. Knowing more about the underlying mechanism can reveal new possibilities for treatment and prevention of genetic disorders like 3-M syndrome.

- One study looks at 33 cases of 3M syndrome, 23 of these cases were identified as CUL7 mutations: 12 being homozygotes and 11 being heterozygotes. This new research shows genetic heterogeneity in 3M syndrome, in contrast to the clinical homogeneity. Additional studies are still ongoing and will lead to the understanding of this new information.

- This study provides more insight on the three genes involved in 3M syndrome and how they interact with each other in normal development. It lead to the discovery that the CUL7, OBS1, and CCDC8 form a complex that functions to maintain microtubule and genomic integrity.