The effects a coloboma has on the vision can be mild or more severe depending on the size and location of the gap. If, for example, only a small part of the iris is missing, vision may be normal, whereas if a large part of the retina or optic nerve is missing, vision may be poor and a large part of the visual field may be missing. This is more likely to cause problems with mobility if the lower visual field is absent. Other conditions can be associated with a coloboma. Sometimes, the eye may be reduced in size, a condition called microphthalmia. Glaucoma, nystagmus, scotoma, or strabismus may also occur.

Other ocular malformations that include coloboma or are related to it:

- CHARGE syndrome, a term that came into use as an acronym for the set of unusual congenital features seen in a number of newborn children. The letters stand for: 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. Although these features are no longer used in making a diagnosis, the name has remained.

- Cat eye syndrome, caused by the short arm (p) and a small section of the long arm (q) of human chromosome 22 being present three (trisomic) or four times (tetrasomic) instead of the usual two times. The term "cat eye" was coined because of the particular appearance of the vertical colobomas in the eyes of some patients.

- Patau syndrome (trisomy 13), a chromosomal abnormality that can cause a number of deformities, some of which include structural eye defects, including microphthalmia, Peters anomaly, cataract, iris and/or fundus coloboma, retinal dysplasia or retinal detachment, sensory nystagmus, cortical visual loss, and optic nerve hypoplasia.

- Treacher Collins syndrome, autosomal dominant syndrome caused by mutation of "TCOF1". Coloboma is part of a set of characteristic facies that features craniofacial malformations, such as downslanting eyes, ear anomalies, or hypoplasia of zygomatic bone and jaw (micrognathia).

Microcoria is a congenital disease in which the pupils of the subject are narrower than 2 mm in diameter. Microcoria is associated with juvenile-onset glaucoma. It is also associated with Pierson syndrome chararacterized by microcoria and congenital nephrotic syndrome. The defect is in the Laminin beta 2 gene on chromosome 3p21 which encodes a protein essential to the glomerular basement membrane.

It is also part of the known manifestations of a born infant to a mother suffering from uncontrolled hyperglycemia. Other symptoms include transposition of great vessels, respiratory distress secondary to surfactant defect, sacral agensis, jitteriness, irritability, and lethargy due to rebound fetal hypoglycemia. Congenital microcoria is an autosomal dominant trait. However, it can also occur sporadically.

An anopsia or anopia is a defect in the visual field. If the defect is only partial, then the portion of the field with the defect can be used to isolate the underlying cause.

Types of partial anopsia:

- Hemianopsia

- Homonymous hemianopsia

- Heteronymous hemianopsia

- Binasal hemianopsia

- Bitemporal hemianopsia

- Superior hemianopia

- Inferior hemianopia

- Quadrantanopia

The term "anopsia" comes from the Ancient Greek ἀν- ("an-"), "un-" and ὄψις ("opsis") "sight".

Cloacal exstrophy (EC) is a severe birth defect wherein much of the abdominal organs (the bladder and intestines) are exposed. It often causes the splitting of both male and female genitalia (specifically, the penis and clitoris respectively), and the anus is occasionally sealed.

Cloacal exstrophy is a rare birth defect, present in 1/200,000 pregnancies and 1/400,000 live births.

It is caused by a defect of the ventral body wall—mesodermal migration is inhibited and folding fails.

Fetal trimethadione syndrome is characterized by the following major symptoms as a result of the teratogenic characteristics of trimethadione.

- Cranial and facial abnormalities which include; microcephaly, midfacial flattening, V-shaped eyebrows and a short nose

- Cardiovascular abnormalities

- Absent kidney and ureter

- Meningocele, a birth defect of the spine

- Omphalocele, a birth defect where portions of the abdominal contents project into the umbilical cord

- A in mental and physical development

Vision in the affected eye is impaired, the degree of which depends on the size of the defect, and typically affects the visual field more than visual acuity. Additionally, there is an increased risk of serous retinal detachment, manifesting in 1/3 of patients. If retinal detachment does occur, it is usually not correctable and all sight is lost in the affected area of the eye, which may or may not involve the macula.

Brunner syndrome is a rare genetic disorder associated with a mutation in the MAOA gene. It is characterized by lower than average IQ (typically about 85), problematic impulsive behavior (such as arson, hypersexuality and violence), sleep disorders and mood swings. It was identified in fourteen males from one family in 1993. It has since been discovered in two additional families.

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.

Tracheal agenesis is a rare birth defect with a prevalence of less than 1 in 50,000, in which the trachea fails to develop. The defect is normally fatal, although occasional cases have been reported of long-term survival following surgical intervention.

There are three main types of tracheal agenesis, designated Types I, II and III.

In 2013, a case was reported of a South Korean child with tracheal agenesis who had been successfully treated after having been kept alive in an intensive care unit for the first two and a half years of her life. She then had an artificially created trachea implanted that had been created by tissue engineering using her own stem cells. The patient however later died from complications.

Southeast Asian ovalocytosis is a blood disorder that is similar to, but distinct from hereditary elliptocytosis. It is common in some communities in Malaysia and Papua New Guinea, as it confers some resistance to cerebral Falciparum Malaria.

Cleidocranial dysostosis is a general skeletal condition so named from the collarbone (cleido-) and cranium deformities which people with it often have.

People with the condition usually present with a painless swelling in the area of the clavicles at 2–3 years of age. Common features are:

- Clavicles (collarbones) can be partly missing leaving only the medial part of the bone. In 10% cases, they are completely missing. If the collarbones are completely missing or reduced to small vestiges, this allows hypermobility of the shoulders including ability to touch the shoulders together in front of the chest. The defect is bilateral 80% of the time. Partial collarbones may cause nerve damage symptoms and therefore have to be removed by surgery.

- The mandible is prognathic due to hypoplasia of maxilla (micrognathism) and other facial bones.

- A soft spot or larger soft area in the top of the head where the fontanelle failed to close, or the fontanelle closes late.

- Bones and joints are underdeveloped. People are shorter and their frames are smaller than their siblings who do not have the condition.

- The permanent teeth include supernumerary teeth. Unless these supernumeraries are removed they will crowd the adult teeth in what already may be an underdeveloped jaw. If so, the supernumeraries will probably need to be removed to make space for the adult teeth. Up to 13 supernumarary teeth have been observed. Teeth may also be displaced. Cementum formation may be deficient.

- Failure of eruption of permanent teeth.

- Bossing (bulging) of the forehead.

- Open skull sutures, large fontanelles.

- Hypertelorism.

- Delayed ossification of bones forming symphysis pubis, producing a widened symphysis.

- Coxa vara can occur, limiting abduction and causing Trendelenburg gait.

- Short middle fifth phalanges, sometimes causing short and wide fingers.

- Vertebral abnormalities.

- On rare occasions, brachial plexus irritation can occur.

- Scoliosis, spina bifida and syringomyelia have also been described.

Other features are: parietal bossing, basilar invagination (atlantoaxial impaction), persistent metopic suture, abnormal ear structures with hearing loss, supernumerary ribs, hemivertebrae with spondylosis, small and high scapulae, hypoplasia of illiac bones, absence of the pubic bone, short / absent fibular bones, short / absent radial bones, hypoplastic terminal phalanges.

Fetal trimethadione syndrome (also known as paramethadione syndrome, German syndrome, tridione syndrome, among others) is a set of birth defects caused by the administration of the anticonvulsants trimethadione (also known as Tridione) or paramethadione to epileptic mothers during pregnancy.

Fetal trimethadione syndrome is classified as a rare disease by the National Institute of Health's Office of Rare Diseases, meaning it affects less than 200,000 individuals in the United States.

The fetal loss rate while using trimethadione has been reported to be as high as 87%.

Rachischisis (Greek: "rhachis - ῥάχις" - spine, and "schisis - σχίσις" - split) is a developmental birth defect involving the neural tube. This anomaly occurs in utero, when the posterior neuropore of the neural tube fails to close by the 27th intrauterine day. As a consequence the vertebrae overlying the open portion of the spinal cord do not fully form and remain unfused and open, leaving the spinal cord exposed. Patients with rachischisis have motor and sensory deficits, chronic infections, and disturbances in bladder function. This defect often occurs with anencephaly.

Craniorachischisis is a variant of rachischisis that occurs when the entire spinal cord and brain are exposed - simultaneous complete rachischisis and anencephaly. It is incompatible with life; affected pregnancies often end in miscarriage or stillbirth. Infants born alive with craniorachischisis die soon after birth.

Relative afferent pupillary defect (RAPD) or Marcus Gunn pupil is a medical sign observed during the swinging-flashlight test whereupon the patient's pupils constrict less (therefore appearing to dilate) when a bright light is swung from the unaffected eye to the affected eye. The affected eye still senses the light and produces pupillary sphincter constriction to some degree, albeit reduced.

The most common cause of Marcus Gunn pupil is a lesion of the optic nerve (between the retina and the optic chiasm) or severe retinal disease. It is named after Scottish ophthalmologist Robert Marcus Gunn.

A second common cause of Marcus Gunn pupil is a contralateral optic tract lesion, due to the different contributions of the intact nasal and temporal hemifields.

Blau Syndrome is an autosomal dominant genetic inflammatory disorder which affects the skin, eyes, and joints. It is caused by a mutation in the NOD2 (CARD15) gene. Symptoms usually begin before the age of 4, and the disease manifests as early onset cutaneous sarcoidosis, granulomatous arthritis, and uveitis.

Progesterone & Rauwolfia Serpentina (containing Reserpine) are a possible treatment as they both increase MAO-A activity.

Asplenia with cardiovascular anomalies, also known as Ivemark syndrome and right atrial isomerism, is an example of a heterotaxy syndrome. These uncommon congenital disorders are characterized by defects in the heart, spleen and paired organs such as the lungs and kidneys. Another name is "asplenia-cardiovascular defect-heterotaxy".

Right atrial isomerism is named for its discoverer, Swedish pathologist Biörn Ivemark.

The syndrome has five characteristic findings:

- Omphalocele

- Anterior diaphragmatic hernia

- Sternal cleft with or without ectopia cordis

- Diaphragmatic pericardium defects (no diaphragmatic pericardium)

- Intracardiac defect: ventricular septal defect, diverticulum of the left ventricle, Tetralogy of Fallot

In right atrial isomerism, both atria of the heart are morphological right atria leading to associated abnormalities in the pulmonary venous system. In addition, individuals with right atrial isomerism develop asplenia, a midline liver, malrotation of the small intestine and the presence of two morphologic right lungs. Individuals with left atrial isomerism, by comparison, have two morphologic left atria, polysplenia, intestinal malrotation and two morphologic left lungs.

The majority of cases present at the time of birth or within a few days or weeks. Presenting signs and symptoms of the congenital heart defect may include cyanosis, breathlessness, lethargy and poor feeding.

The Marcus Gunn pupil is a relative afferent pupillary defect indicating a decreased pupillary response to light in the affected eye.

In the swinging flashlight test, a light is alternately shone into the left and right eyes. A normal response would be equal constriction of both pupils, regardless of which eye the light is directed at. This indicates an intact direct and consensual pupillary light reflex. When the test is performed in an eye with an afferent pupillary defect, light directed in the affected eye will cause only mild constriction of both pupils (due to decreased response to light from the afferent defect), while light in the unaffected eye will cause a normal constriction of both pupils (due to an intact efferent path, and an intact consensual pupillary reflex). Thus, light shone in the affected eye will produce less pupillary constriction than light shone in the unaffected eye.

A Marcus Gunn pupil is distinguished from a total CN II lesion, in which the affected eye perceives "no" light. In that case, shining the light in the affected eye produces no effect.

Anisocoria is absent. A Marcus Gunn pupil is seen, among other conditions, in optic neuritis. It is also common in retrobulbar optic neuritis due to multiple sclerosis but only for 3–4 weeks, until the visual acuity begins to improve in 1–2 weeks and may return to normal.

The sac, which is formed from an outpouching of peritoneum, protrudes in the midline, through the umbilicus (navel).

It is normal for the intestines to protrude from the abdomen, into the umbilical cord, until about the tenth week of pregnancy, after which they return to inside the fetal abdomen.

The omphalocele can be mild, with only a small loop of intestines present outside the abdomen, or severe, containing most of the abdominal organs. In severe cases surgical treatment is made more difficult because the infant's abdomen is abnormally small, having had no need to expand to accommodate the developing organs.

Larger omphalocele are associated with a higher risk of cardiac defects.

Caused by malrotation of the bowels while returning to the abdomen during development. Some cases of omphalocele are believed to be due to an underlying genetic disorder, such as Edward's syndrome (trisomy 18) or Patau syndrome (trisomy 13).

Beckwith–Wiedemann syndrome is also associated with omphaloceles.

Aortopulmonary window refers to a congenital heart defect similar in some ways to persistent truncus arteriosus. Persistent truncus arteriosus involves a single valve; aortopulmonary window is a septal defect.

Signs and symptoms are related to type and severity of the heart defect. Symptoms frequently present early in life, but it is possible for some CHDs to go undetected throughout life. Some children have no signs while others may exhibit shortness of breath, cyanosis, fainting, heart murmur, under-development of limbs and muscles, poor feeding or growth, or respiratory infections. Congenital heart defects cause abnormal heart structure resulting in production of certain sounds called heart murmur. These can sometimes be detected by auscultation; however, not all heart murmurs are caused by congenital heart defects.