National Center for Advancing and Translational Sciences Genetic and Rare Diseases Information Center, a program of the National Center for Advancing and Translational Sciences

Syndromic microphthalmia, type 3



Other Names:
MCOPS3; Microphthalmia and esophageal atresia syndrome; Anophthalmia clinical with associated anomalies; MCOPS3; Microphthalmia and esophageal atresia syndrome; Anophthalmia clinical with associated anomalies; Anophthalmia esophageal genital syndrome; AEG syndrome; Anophthalmia microphthalmia esophageal atresia; SOX2 anophthalmia syndrome; SOX2-related eye disorders See More
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This disease is grouped under:

Syndromic microphthalmia, type 3 is a rare condition that affects the eyes and other parts of the body. Babies with this condition are generally born without eyeballs (anophthalmia) or with eyes that are unusually small (microphthalmia). Both of these abnormalities can be associated with severe vision loss. Other signs and symptoms of syndromic microphthalmia, type 3 may include seizures, brain malformations, esophageal atresia, delayed motor development, learning disabilities, and sensorineural hearing loss. The condition is caused by changes (mutations) in the SOX2 gene and is inherited in an autosomal dominant manner.[1][2][3] Treatment is based on the signs and symptoms present in each person.[3]
Last updated: 2/29/2016

This table lists symptoms that people with this disease may have. For most diseases, symptoms will vary from person to person. People with the same disease may not have all the symptoms listed. This information comes from a database called the Human Phenotype Ontology (HPO) . The HPO collects information on symptoms that have been described in medical resources. The HPO is updated regularly. Use the HPO ID to access more in-depth information about a symptom.

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Medical Terms Other Names
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HPO ID
80%-99% of people have these symptoms
Anophthalmia
Absence of eyeballs
Failure of development of eyeball
Missing eyeball
No eyeball
[ more ]
0000528
Esophageal atresia
Birth defect in which part of esophagus did not develop
0002032
Microphthalmia
Abnormally small eyeball
0000568
Tracheoesophageal fistula 0002575
30%-79% of people have these symptoms
Agenesis of corpus callosum 0001274
Cryptorchidism
Undescended testes
Undescended testis
[ more ]
0000028
Hearing impairment
Deafness
Hearing defect
[ more ]
0000365
Visual loss
Loss of vision
Vision loss
[ more ]
0000572
5%-29% of people have these symptoms
11 pairs of ribs 0000878
Global developmental delay 0001263
Growth delay
Delayed growth
Growth deficiency
Growth failure
Growth retardation
Poor growth
Retarded growth
[ more ]
0001510
Hemivertebrae
Missing part of vertebrae
0002937
Holoprosencephaly 0001360
Hydrocephalus
Too much cerebrospinal fluid in the brain
0000238
Hypoplasia of penis
Underdeveloped penis
0008736
Hypospadias 0000047
Intellectual disability
Mental deficiency
Mental retardation
Mental retardation, nonspecific
Mental-retardation
[ more ]
0001249
Iris coloboma
Cat eye
0000612
Patent ductus arteriosus 0001643
Sclerocornea
Hardening of skin and connective tissue
0000647
Ventricular septal defect
Hole in heart wall separating two lower heart chambers
0001629
Percent of people who have these symptoms is not available through HPO
Anterior pituitary hypoplasia
Underdeveloped pituitary gland
0010627
Autosomal dominant inheritance 0000006
Butterfly vertebrae 0003316
Coloboma
Notched pupil
0000589
Frontal bossing 0002007
Generalized hypotonia
Decreased muscle tone
Low muscle tone
[ more ]
0001290
Hypogonadotropic hypogonadism 0000044
Hypoplasia of the corpus callosum
Underdevelopment of part of brain called corpus callosum
0002079
Hypothalamic hamartoma 0002444
Microcephaly
Abnormally small skull
Decreased circumference of cranium
Decreased size of skull
Reduced head circumference
Small head circumference
[ more ]
0000252
Micropenis
Short penis
Small penis
[ more ]
0000054
Missing ribs
Absent ribs
Decreased rib number
[ more ]
0000921
Muscular hypotonia
Low or weak muscle tone
0001252
Optic nerve hypoplasia 0000609
Postnatal growth retardation
Growth delay as children
0008897
Rib fusion
Fused ribs
0000902
Sensorineural hearing impairment 0000407
Short stature
Decreased body height
Small stature
[ more ]
0004322
Spastic diplegia 0001264
Spastic tetraplegia 0002510
Specific learning disability 0001328
Supernumerary ribs
Extra ribs
0005815
Vertebral fusion
Spinal fusion
0002948
Vertebral hypoplasia
Underdeveloped vertebrae
0008417
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Last updated: 7/1/2020

Making a diagnosis for a genetic or rare disease can often be challenging. Healthcare professionals typically look at a person’s medical history, symptoms, physical exam, and laboratory test results in order to make a diagnosis. The following resources provide information relating to diagnosis and testing for this condition. If you have questions about getting a diagnosis, you should contact a healthcare professional.

Testing Resources

  • The Genetic Testing Registry (GTR) provides information about the genetic tests for this condition. The intended audience for the GTR is health care providers and researchers. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.

If you need medical advice, you can look for doctors or other healthcare professionals who have experience with this disease. You may find these specialists through advocacy organizations, clinical trials, or articles published in medical journals. You may also want to contact a university or tertiary medical center in your area, because these centers tend to see more complex cases and have the latest technology and treatments.

If you can’t find a specialist in your local area, try contacting national or international specialists. They may be able to refer you to someone they know through conferences or research efforts. Some specialists may be willing to consult with you or your local doctors over the phone or by email if you can't travel to them for care.

You can find more tips in our guide, How to Find a Disease Specialist. We also encourage you to explore the rest of this page to find resources that can help you find specialists.

Healthcare Resources


Support and advocacy groups can help you connect with other patients and families, and they can provide valuable services. Many develop patient-centered information and are the driving force behind research for better treatments and possible cures. They can direct you to research, resources, and services. Many organizations also have experts who serve as medical advisors or provide lists of doctors/clinics. Visit the group’s website or contact them to learn about the services they offer. Inclusion on this list is not an endorsement by GARD.

Organizations Supporting this Disease


These resources provide more information about this condition or associated symptoms. The in-depth resources contain medical and scientific language that may be hard to understand. You may want to review these resources with a medical professional.

Where to Start

  • Genetics Home Reference (GHR) contains information on Syndromic microphthalmia, type 3. This website is maintained by the National Library of Medicine.

In-Depth Information

  • GeneReviews provides current, expert-authored, peer-reviewed, full-text articles describing the application of genetic testing to the diagnosis, management, and genetic counseling of patients with specific inherited conditions.
  • The Monarch Initiative brings together data about this condition from humans and other species to help physicians and biomedical researchers. Monarch’s tools are designed to make it easier to compare the signs and symptoms (phenotypes) of different diseases and discover common features. This initiative is a collaboration between several academic institutions across the world and is funded by the National Institutes of Health. Visit the website to explore the biology of this condition.
  • Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders. Each entry has a summary of related medical articles. It is meant for health care professionals and researchers. OMIM is maintained by Johns Hopkins University School of Medicine. 
  • Orphanet is a European reference portal for information on rare diseases and orphan drugs. Access to this database is free of charge.
  • PubMed is a searchable database of medical literature and lists journal articles that discuss Syndromic microphthalmia, type 3. Click on the link to view a sample search on this topic.

Questions sent to GARD may be posted here if the information could be helpful to others. We remove all identifying information when posting a question to protect your privacy. If you do not want your question posted, please let us know.


  1. MICROPHTHALMIA, SYNDROMIC 3. OMIM. August 2015; http://www.omim.org/entry/206900.
  2. SOX2 anophthalmia syndrome. Genetics Home Reference. March 2009; http://ghr.nlm.nih.gov/condition/sox2-anophthalmia-syndrome.
  3. Kathleen A Williamson, PhD and David R FitzPatrick, MD, FRCP(EDIN). SOX2-Related Eye Disorders. GeneReviews. July 2014; http://www.ncbi.nlm.nih.gov/books/NBK1300.