Symptoms of holoprosencephaly range from mild (no facial/organ defects, anosmia, or only a single central incisor) to moderate to severe (cyclopia).

There are four classifications of holoprosencephaly.

- Alobar holoprosencephaly, the most serious form, in which the brain fails to separate, is usually associated with severe facial anomalies, including lack of a nose and the eyes merged to a single median structure, see Cyclopia

- Semilobar holoprosencephaly, in which the brain's hemispheres have somewhat divided, is an intermediate form of the disease.

- Lobar holoprosencephaly, in which there is considerable evidence of separate brain hemispheres, is the least severe form. In some cases of lobar holoprosencephaly, the patient's brain may be nearly normal.

- Syntelencephaly, or middle interhemispheric variant of holoprosencephaly (MIHV), in which the posterior frontal lobe and the parietal lobe are not properly separated, but the rostrobasal forebrain properly separates; it is possible that this is not a variant of HPE at all, but is currently classified as such.

- Agenesis of the corpus callosum, in which there is a complete or partial absence of the corpus callosum. It occurs when the corpus callosum, the band of white matter connecting the two hemispheres in the brain, fails to develop normally, typically during pregnancy. The fibers that would otherwise form the corpus callosum become longitudinally oriented within each hemisphere and form structures called Probst bundles.

Holoprosencephaly consists of a spectrum of defects or malformations of the brain and face. At the most severe end of this spectrum are cases involving serious malformations of the brain, malformations so severe that they often cause miscarriage or stillbirth. At the other end of the spectrum are individuals with facial defects which may affect the eyes, nose, and upper lip - and normal or near-normal brain development. Seizures and mental retardation may occur.

The most severe of the facial defects (or anomalies) is cyclopia, an abnormality characterized by the development of a single eye, located in the area normally occupied by the root of the nose, and a missing nose or a nose in the form of a proboscis (a tubular appendage) located above the eye. The condition is also referred to as cyclocephaly or synophthalmia, and is very rare.

Holoprosencephaly (HPE) is a cephalic disorder in which the prosencephalon (the forebrain of the embryo) fails to develop into two hemispheres. Normally, the forebrain is formed and the face begins to develop in the fifth and sixth weeks of human pregnancy. The condition also occurs in other species.

The condition can be mild or severe. According to the National Institute of Neurological Disorders and Stroke (NINDS), "in most cases of holoprosencephaly, the malformations are so severe that babies die before birth."

When the embryo's forebrain does not divide to form bilateral cerebral hemispheres (the left and right halves of the brain), it causes defects in the development of the face and in brain structure and function.

In less severe cases, babies are born with normal or near-normal brain development and facial deformities that may affect the eyes, nose, and upper lip.

Affected newborns generally have striking neurological defects and seizures. Severely impaired development is common, but disturbances in motor functions may not appear until later in life.

Infants with microcephaly are born with either a normal or reduced head size. Subsequently, the head fails to grow, while the face continues to develop at a normal rate, producing a child with a small head and a receding forehead, and a loose, often wrinkled scalp. As the child grows older, the smallness of the skull becomes more obvious, although the entire body also is often underweight and dwarfed. Development of motor functions and speech may be delayed. Hyperactivity and intellectual disability are common occurrences, although the degree of each varies. Convulsions may also occur. Motor ability varies, ranging from in some to spastic quadriplegia in others.

Usually the cerebellum and brain stem are formed normally, although in some cases the cerebellum may also be absent. An infant with hydranencephaly may appear normal at birth or may have some distortion of the skull and upper facial features due to fluid pressure inside the skull. The infant's head size and spontaneous reflexes such as sucking, swallowing, crying, and moving the arms and legs may all seem normal, depending on the severity of the condition. However, after a few weeks the infant sometimes becomes irritable and has increased muscle tone (hypertonia). After several months of life, seizures and hydrocephalus may develop, if they did not exist at birth. Other symptoms may include visual impairment, lack of growth, deafness, blindness, spastic quadriparesis (paralysis), and intellectual deficits.

Some infants may have additional abnormalities at birth including seizures, myoclonus (involuntary sudden, rapid jerks), limited thermoregulation abilities, and respiratory problems.

Still other infants display no obvious symptoms at birth, going many months without a confirmed diagnosis of hydranencephaly. In some cases a severe hydrocephalus, or other cephalic condition, is misdiagnosed.

Microcephaly is a type of cephalic disorder. It has been classified in two types based on the onset:

Additional symptoms include:

- anencephaly (failure of major sections of the brain to form)

- encephalocele (cranial contents protrudes from the skull)

- cyclopia (the two eye cavities fuse into one)

- agnathia

- cleft palate

- arthrogryposis

- clubfeet

- holoprosencephaly

- spina bifida

- low-set ears

- pulmonary hypoplasia

- omphalocele

- gastroschisis

- cardiovascular disorders

- diaphragmatic hernias

- gastrointestinal atresia

- single umbilical artery

- renal abnormalities

- genu recurvatum

- hydramnios

Ethmocephaly is a type of cephalic disorder caused by holoprosencephaly. Ethmocephaly is the least common facial anomaly. It consists of a proboscis separating narrow-set eyes with an absent nose and microphthalmia (abnormal smallness of one or both eyes). Cebocephaly, another facial anomaly, is characterized by a small, flattened nose with a single nostril situated below incomplete or underdeveloped closely set eyes.

The least severe in the spectrum of facial anomalies is the median cleft lip, also called premaxillary agenesis.

Although the causes of most cases of holoprosencephaly remain unknown, some may be due to dominant or chromosome causes. Such chromosomal anomalies as trisomy 13 and trisomy 18 have been found in association with holoprosencephaly, or other neural tube defects. Genetic counseling and genetic testing, such as amniocentesis, is usually offered during a pregnancy if holoprosencephaly is detected. The recurrence risk depends on the underlying cause. If no cause is identified and the fetal chromosomes are normal, the chance to have another pregnancy affected with holoprosencephaly is about 6%.

There is no treatment for holoprosencephaly and the prognosis for individuals with the disorder is poor. Most of those who survive show no significant developmental gains. For children who survive, treatment is symptomatic. It is possible that improved management of diabetic pregnancies may help prevent holoprosencephaly, however there is no means of primary prevention.

The affected infant tends to be short, with a disproportionately large head. The fetal head of Infants born with iniencephaly are hyperextended while the foramen magnum is enlarged and opens through the widened pedicles. The defective neural arches directly into the upper cervical reach of the spinal canal, causing the formation of a common cavity between most of the spinal cord and the brain. The skin of the anterior chest is connected directly to the face, bypassing the formation of a neck, while the scalp is directly connected to the skin of the back. Because of this, those born with this anomaly either have a highly shortened neck or no neck at all. This causes extreme retroflexion, or backward bending, of the head in a "star-gazing" fashion. The spine is severely distorted as well along with significant shortening due to marked lordosis. The vertebrae, especially cervical, are fused together in abnormal shapes and their numbers are reduced. The spinal cord is almost always defective while the ventricular system is often dilated and the cortex is thinned. Sometimes, in the case of iniencephaly apertus, an encephalocele (sac-like protrusions of the brain through an opening in the cranium) forms.

The optic nerve hypoplasia is generally manifested by nystagmus (involuntary eye movements, often side-to-side) and a smaller-than-usual optic disc. The degree of visual impairment is variable, and ranges from normal vision to complete blindness. When nystagmus develops, it typically appears by 1–8 months of age, and usually indicates that there will be a significant degree of visual impairment, but the severity is difficult to predict in infancy. Although there are many measures to compensate for visual impairment, there are few treatments available to induce normal optic nerve function.

Hydranencephaly or hydrancephaly is a condition in which the brain's cerebral hemispheres are absent to varying degrees and the remaining cranial cavity is filled with cerebrospinal fluid.

Hydranencephaly (or hydrancephaly) is a type of cephalic disorder.

These disorders are congenital conditions that derive from either damage to, or abnormal development of, the fetal nervous system in the earliest stages of development in utero. Cephalic is the medical term for “head” or “head end of body.” These conditions do not have any definitive identifiable cause factor; instead generally attributed to a variety of hereditary or genetic conditions, but also by environmental factors such as maternal infection, pharmaceutical intake, or even exposure to high levels of radiation.

This should not be confused with hydrocephalus, which is an accumulation of excess cerebrospinal fluid in the ventricles of the brain.

In hemihydranencephaly, only half of the cranial cavity is filled with fluid.

The brain effects are also variable. Seizures sometimes occur. Prediction of intellectual outcome in infancy is difficult. Various types of early intervention or equivalent programs can help a child reach full developmental potential.

Many organ systems are affected by triploidy, but the central nervous system and skeleton are the most severely affected. Common central nervous system defects seen in triploidy include holoprosencephaly, hydrocephalus (increased amount of cerebrospinal fluid within the brain), ventriculomegaly, Arnold-Chiari malformation, agenesis of the corpus callosum, and neural tube defects. Skeletal manifestations include cleft lip/palate, hypertelorism, club foot, and syndactyly of fingers three and four. Congenital heart defects, hydronephrosis, omphalocele, and meningocele (spina bifida) are also common. Cystic hygromas occur but are uncommon. Triploid fetuses have intrauterine growth restriction beginning early in the pregnancy, as early as 12 weeks, and does not affect the head as severely as the body. Oligohydramnios, low levels of amniotic fluid, is common in triploid pregnancies.

Placental abnormalities are common in triploidy. Most frequently, the placenta is enlarged and may have cysts within. In some cases, the placenta may be unusually small, having ceased to grow.

Where known, the ICD-10 code is listed below.

- Anencephaly (Q00.0)

- Colpocephaly (ICD10 unknown)

- Holoprosencephaly (Q04.2)

- Ethmocephaly (ICD10 unknown)

- Hydranencephaly (Q04.3)

- Iniencephaly (Q00.2)

- Lissencephaly (Q04.3)

- Megalencephaly (Q04.5)

- Microcephaly (Q02)

- Porencephaly (Q04.6)

- Schizencephaly (Q04.6)

In some children without “classic” holoprosencephaly, microforms of holoprosencephaly may be noted on MRI, including missing olfactory tracts and bulbs and absent or hypoplastic corpus callosum.

Cerebellar agenesis is a rare condition in which a brain develops without the cerebellum. The cerebellum controls smooth movement, and when it does not develop, the rest of the brain must compensate, which it cannot do completely. The condition is not fatal on its own, but people born without a cerebellum experience severe developmental delays, language deficits, and neurological abnormalities. As children with cerebellar agenesis get older, their movements usually improve. It can co-exist with other severe malformations of the central nervous system, like anencephaly, holoprosencephaly, and microencephaly.

The condition was first reported in 1831. 10 cases had been reported as of 1998. Agenesis of one half or another part of the cerebellum is more common than complete agenesis.

Cerebellar agenesis can be caused by mutations in the PTF1A gene.

Cebocephaly [Greek "kebos", monkey + "kephale", head] is a developmental anomaly of the head characterized by a monkey-like head, with a defective small, flattened nose with a single nostril or absent nose and closely set eyes. Cebocephaly is part of a group of defects called holoprosencephaly. The incidence of cebocephaly is 1 in 16,000 births.

Cognitive ability in individuals with 18p- varies widely, with most falling in the mild to moderate range of impairment, though there have been some reports of people with impairment in the severe to profound range. These individuals may have had holoprosencephaly, which is frequently associated with severe impairment.

Speech deficits are quite common within this population. Frequently, expressive speech lags behind other developmental parameters.

There are two problems that may occur during development that cause acrania.

Cephalic disorders (from the Greek word "κεφάλι", meaning "head") are congenital conditions that stem from damage to, or abnormal development of, the budding nervous system. Cephalic means "head" or "head end of the body."

Cephalic disorders are not necessarily caused by a single factor, but may be influenced by hereditary or genetic conditions, nutritional deficiencies, or by environmental exposures during pregnancy, such as medication taken by the mother, maternal infection, or exposure to radiation. Some cephalic disorders occur when the cranial sutures (the fibrous joints that connect the bones of the skull) join prematurely. Most cephalic disorders are caused by a disturbance that occurs very early in the development of the fetal nervous system.

The human nervous system develops from a small, specialized plate of cells on the surface of the embryo. Early in development, this plate of cells forms the neural tube, a narrow sheath that closes between the third and fourth weeks of pregnancy to form the brain and spinal cord of the embryo. Four main processes are responsible for the development of the nervous system: cell proliferation, the process in which nerve cells divide to form new generations of cells; cell migration, the process in which nerve cells move from their place of origin to the place where they will remain for life; cell differentiation, the process during which cells acquire individual characteristics; and cell death, a natural process in which cells die.

Damage to the developing nervous system is a major cause of chronic, disabling disorders and, sometimes, death in infants, children, and even adults. The degree to which damage to the developing nervous system harms the mind and body varies enormously. Many disabilities are mild enough to allow those afflicted to eventually function independently in society. Others are not. Some infants, children, and adults die, others remain totally disabled, and an even larger population is partially disabled, functioning well below normal capacity throughout life.

The National Institute of Neurological Disorders and Stroke (NINDS) is currently "conducting and supporting research on normal and abnormal brain and nervous system development."

Triploid syndrome, also called triploidy, is an extremely rare chromosomal disorder, in which a fetus has three copies of every chromosome instead of the normal two. If this occurs in only some cells, it is called mosaic triploidy, and is less severe.

Acrania is a rare congenital disorder that occurs in the human fetus in which the flat bones in the cranial vault are either completely or partially absent. The cerebral hemispheres develop completely but abnormally. The condition is frequently, though not always, associated with anencephaly. The fetus is said to suffer from acrania if it meets the following criteria: the fetus should have a perfectly normal facial bone, a normal cervical column but without the fetal skull and a volume of brain tissue equivalent to at least one third of the normal brain size.

Cyclopia (also cyclocephaly or synophthalmia) is a rare form of holoprosencephaly and is a congenital disorder (birth defect) characterized by the failure of the embryonic prosencephalon to properly divide the orbits of the eye into two cavities. Its incidence is 1 in 16,000 in born animals and 1 in 200 in miscarried fetuses.

13q deletion syndrome is a rare genetic disease caused by the deletion of some or all of the large arm of human chromosome 13. It causes intellectual disability and congenital malformations that affect a variety of organ systems.

Different areas of deletion are associated with different symptoms. Deletions from the centromere to 13q32 or any deletions including the 13q32 band are associated with slow growth, intellectual disability, and congenital malformations. Deletions from 13q33 to the end of the chromosome are associated with intellectual disability. Intellectual disabilities range from very mild to very severe, and can co-occur with behavioral disorders and/or autism spectrum disorders.

At birth, the main symptoms include low weight (due to intrauterine growth restriction), hypotonia, and feeding difficulties. Infants may also have cleft palate.

13q deletion syndrome gives a characteristic appearance to affected individuals, potentially including microphthalmia (small eyes), hypertelorism (wide-set eyes), thin forehead, high palate, underdeveloped midface, small mouth, small nose, broad, flat nasal bridge, short neck, low hairline, irregular or wrongly positioned teeth, low-set ears, micrognathia (small jaw), tooth enamel defects, short stature, microcephaly (small head), a prominent, long philtrum, and earlobes turned inwards.

Congenital heart disease is associated with 13q deletion syndrome. Common defects include atrial septal defect, tetralogy of Fallot, ventricular septal defect, patent ductus arteriosus, pulmonary stenosis, and coarctation of the aorta. Defects of the endocrine system, digestive system, and genitourinary system are also common. These include underdevelopment or agenesis of the pancreas, adrenal glands, thymus, gallbladder, and thyroid; Hirschsprung's disease; gastric reflux, imperforate anus, retention testis, ectopic kidney, renal agenesis, and hydronephrosis.

A variety of brain abnormalities are also associated with 13q deletion. They can include epilepsy, craniosynostosis (premature closing of the skull bones), spastic diplegia, cerebral hypotrophy, underdevelopment or agenesis of the corpus callosum, cerebellar hypoplasia, deafness, and, rarely, hydrocephalus, Dandy–Walker syndrome, and spina bifida. The eyes can be severely damaged and affected individuals may be blind. They may also have coloboma of the iris or choroid, strabismus, nystagmus, glaucoma, or cataracts.

Other skeletal malformations are found with 13q deletion syndrome, including syndactyly, clubfoot, clinodactyly, and malformations of the vertebrae and/or thumbs.

Deletions that include the 13q32 band, which contains the brain development gene ZIC2, are associated with holoprosencephaly; they are also associated with hand and foot malformations. Deletions that include the 13q14 band, which contains the tumor suppressor gene Rb, are associated with a higher risk of developing retinoblastoma, which is more common in XY children. Deletion of the 13q33.3 band is associated with hypospadias. Other genes in the potentially affected region include NUFIP1, HTR2A, PDCH8, and PCDH17.

Typically, the nose is either missing or replaced with a non-functional nose. This deformity (called proboscis) usually forms above the center eye or on the back, and is characteristic of a form of cyclopia called rhinencephaly or rhinocephaly. Most such embryos are either naturally aborted or are stillborn upon delivery.

Although cyclopia is rare, several cyclopic human babies are preserved in medical museums (e.g. The Vrolik Museum, Amsterdam, Trivandrum Medical College).

Some extreme cases of cyclopia have been documented in farm animals (horses, sheep, pigs, and sometimes chickens). In such cases, the nose and mouth fail to form, or the nose grows from the roof of the mouth obstructing airflow, resulting in suffocation shortly after birth.