Studies have shown that obesity of the mother increases the risk of neural tube disorders such as iniencephaly by 1.7 fold while severe obesity increases the risk by over 3 fold.

Once a mother has given birth to a child with iniencephaly, risk of reoccurrence increases to 1-5%.

Numerous possible risk factors have been identified, including gestational diabetes, transplacental infections (the "TORCH complex"), first trimester bleeding, and a history of miscarriage. As well, the disorder is found twice as often in female babies. However, there appears to be no correlation between HPE and maternal age.

There is evidence of a correlation between HPE and the use of various drugs classified as being potentially unsafe for pregnant and lactating mothers. These include insulin, birth control pills, aspirin, lithium, thorazine, retinoic acid, and anticonvulsants. There is also a correlation between alcohol consumption and HPE, along with nicotine, the toxins in cigarettes and toxins in cigarette smoke when used during pregnancy.

Prognosis is poor. Previous research suggested a 100% mortality rate for those with acrania. This disease is rare, occurring in 1 in 20,000 live births.

In order to better manage an acrania diagnosis, early detection is of extreme importance so that actions may be taken to help the mother and child. Families may choose either to terminate the pregnancy, or to carry the child to term. Acrania may cause a fetus to spontaneously abort before reaching term.

In utero exposure to cocaine and other street drugs can lead to septo-optic dysplasia.

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.

There is still some discussion on whether FND is sporadic or genetic. The majority of FND cases are sporadic. Yet, some studies describe families with multiple members with FND. Gene mutations are likely to play an important role in the cause. Unfortunately, the genetic cause for most types of FND remains undetermined.

Rare familial recurrence has been reported, suggesting at least one genetic form (HESX1). In addition to HESX1, mutations in OTX2, SOX2 and PAX6 have been implicated in de Morsier syndrome, but in most cases SOD is a sporadic birth defect of unknown cause and does not recur with subsequent pregnancies.

Little genetic counseling can be offered for acrania because the genetic origins are not fully understood. In order to make genetic counseling for families easier this disease is often differentially diagnosed with other diseases that can occur at the same time such as anencephaly and acalvaria, though these diseases may not always occur simultaneously. While this disease is tragic, reoccurrence rates are extremely low so genetic counseling is not always necessary.

Genetic

- Inborn errors of metabolism

1. Congenital disorder of glycosylation

2. Mitochondrial disorders

3. Peroxisomal disorder

4. Glucose transporter defect

5. Menkes disease

6. Congenital disorders of amino acid metabolism

7. Organic acidemia

Syndromes

- Contiguous gene deletion

1. 17p13.3 deletion (Miller–Dieker syndrome)

- Single gene defects

1. Rett syndrome (primarily girls)

2. Nijmegen breakage syndrome

3. X-linked lissencephaly with abnormal genitalia

4. Aicardi–Goutières syndrome

5. Ataxia telangiectasia

6. Cohen syndrome

7. Cockayne syndrome

Acquired

- Disruptive injuries

1. Traumatic brain injury

2. Hypoxic-ischemic encephalopathy

3. Ischemic stroke

4. Hemorrhagic stroke

- Infections

1. Congenital HIV encephalopathy

2. Meningitis

3. Encephalitis

- Toxins

1. Lead poisoning

2. Chronic renal failure

- Deprivation

1. Hypothyroidism

2. Anemia

3. Congenital heart disease

4. Malnutrition

Genetic factors may play a role in causing some cases of microcephaly. Relationships have been found between autism, duplications of chromosomes, and macrocephaly on one side. On the other side, a relationship has been found between schizophrenia, deletions of chromosomes, and microcephaly. Moreover, an association has been established between common genetic variants within known microcephaly genes ("MCPH1, CDK5RAP2") and normal variation in brain structure as measured with magnetic resonance imaging (MRI)i.e., primarily brain cortical surface area and total brain volume.

The spread of Aedes mosquito-borne Zika virus has been implicated in increasing levels of congenital microcephaly by the International Society for Infectious Diseases and the US Centers for Disease Control and Prevention. Zika can spread from a pregnant woman to her fetus. This can result in other severe brain malformations and birth defects. A study published in The New England Journal of Medicine has documented a case in which they found evidence of the Zika virus in the brain of a fetus that displayed the morphology of microcephaly.

In utero exposure to cocaine and other street drugs can lead to hydranencephaly.

Isolated

1. Familial (autosomal recessive) microcephaly

2. Autosomal dominant microcephaly

3. X-linked microcephaly

4. Chromosomal (balanced rearrangements and ring chromosome)

Syndromes

- Chromosomal

1. Poland syndrome

2. Down syndrome

3. Edward syndrome

4. Patau syndrome

5. Unbalanced rearrangements

- Contiguous gene deletion

1. 4p deletion (Wolf–Hirschhorn syndrome)

2. 5p deletion (Cri-du-chat)

3. 7q11.23 deletion (Williams syndrome)

4. 22q11 deletion (DiGeorge syndrome)

- Single gene defects

1. Smith–Lemli–Opitz syndrome

2. Seckel syndrome

3. Cornelia de Lange syndrome

4. Holoprosencephaly

5. Primary microcephaly 4

6. Wiedemann-Steiner syndrome

Acquired

- Disruptive injuries

1. Ischemic stroke

2. Hemorrhagic stroke

3. Death of a monozygotic twin

- Vertically transmitted infections

1. Congenital cytomegalovirus infection

2. Toxoplasmosis

3. Congenital rubella syndrome

4. Zika virus

- Drugs

1. Fetal hydantoin syndrome

2. Fetal alcohol syndrome

Other

1. Radiation exposure to mother

2. Maternal malnutrition

3. Maternal phenylketonuria

4. Poorly controlled gestational diabetes

5. Hyperthermia

6. Maternal hypothyroidism

7. Placental insufficiency

OAFNS is a combination of FND and oculo-auriculo-vertebral spectrum (OAVS).

The diagnosis of OAVS is based on the following facial characteristics: microtia (underdeveloped external ear), preauricular tags, facial asymmetry, mandibular hypoplasia and epibulbar lipodermoids (benign tumor of the eye which consists of adipose and fibrous tissue).

There still remains discussion about the classification and the minimal amount of characteristics. When someone presents with FND and the characteristics of OAVS, the diagnosis OAFNS may be made.

As the incidence of OAFNS is unknown, there are probably a lot of children with mild phenotypes that aren’t being diagnosed as being OAFNS.

The cause of OAFNS is unknown, but there are some theories about the genesis. Autosomal recessive inheritance is suggested because of a case with two affected siblings and a case with consanguineous parents. However, another study shows that it is more plausible that OAFNS is sporadic.

It is known that maternal diabetes plays a role in developing malformations of craniofacial structures and in OAVS. Therefore, it is suggested as a cause of OAFNS. Folate deficiency is also suggested as possible mechanism.

Low-dose CT protocols should be considered in diagnosing children with OAFNS.

As a recessive genetic condition, both parents must carry the asymptomatic gene and pass it along to their child, a chance of 25 percent. Despite determination of cause, hydranencephaly afflicts both males and females in equal numbers.

A low socioeconomic status in a deprived neighborhood may include exposure to “environmental stressors and risk factors.” Socioeconomic inequalities are commonly measured by the Cartairs-Morris score, Index of Multiple Deprivation, Townsend deprivation index, and the Jarman score. The Jarman score, for example, considers “unemployment, overcrowding, single parents, under-fives, elderly living alone, ethnicity, low social class and residential mobility.” In Vos’ meta-analysis these indices are used to view the effect of low SES neighborhoods on maternal health. In the meta-analysis, data from individual studies were collected from 1985 up until 2008. Vos concludes that a correlation exists between prenatal adversities and deprived neighborhoods. Other studies have shown that low SES is closely associated with the development of the fetus in utero and growth retardation. Studies also suggest that children born in low SES families are “likely to be born prematurely, at low birth weight, or with asphyxia, a birth defect, a disability, fetal alcohol syndrome, or AIDS.” Bradley and Corwyn also suggest that congenital disorders arise from the mother’s lack of nutrition, a poor lifestyle, maternal substance abuse and “living in a neighborhood that contains hazards affecting fetal development (toxic waste dumps).” In a meta-analysis that viewed how inequalities influenced maternal health, it was suggested that deprived neighborhoods often promoted behaviors such as smoking, drug and alcohol use. After controlling for socioeconomic factors and ethnicity, several individual studies demonstrated an association with outcomes such as perinatal mortality and preterm birth.

While not always pathological, it can present as a birth defect in multiple syndromes including:

- Catel–Manzke syndrome

- Bloom syndrome

- Coffin–Lowry syndrome

- congenital rubella

- Cri du chat syndrome

- DiGeorge's syndrome

- Ehlers-Danlos syndrome

- fetal alcohol syndrome

- Hallermann-Streiff syndrome

- Hemifacial microsomia (as part of Goldenhar syndrome)

- Juvenile idiopathic arthritis

- Marfan syndrome

- Noonan syndrome

- Pierre Robin syndrome

- Prader–Willi syndrome

- Progeria

- Russell-Silver syndrome

- Seckel syndrome

- Smith-Lemli-Opitz syndrome

- Treacher Collins syndrome

- Trisomy 13 (Patau syndrome)

- Trisomy 18 (Edwards syndrome)

- Wolf–Hirschhorn syndrome

- X0 syndrome (Turner syndrome)

Substances whose toxicity can cause congenital disorders are called "teratogens", and include certain pharmaceutical and recreational drugs in pregnancy as well as many environmental toxins in pregnancy.

A review published in 2010 identified 6 main teratogenic mechanisms associated with medication use: folate antagonism, neural crest cell disruption, endocrine disruption, oxidative stress, vascular disruption and specific receptor- or enzyme-mediated teratogenesis.

It is estimated that 10% of all birth defects are caused by prenatal exposure to a teratogenic agent. These exposures include, but are not limited to, medication or drug exposures, maternal infections and diseases, and environmental and occupational exposures. Paternal smoking use has also been linked to an increased risk of birth defects and childhood cancer for the offspring, where the paternal germline undergoes oxidative damage due to cigarette use. Teratogen-caused birth defects are potentially preventable. Studies have shown that nearly 50% of pregnant women have been exposed to at least one medication during gestation. During pregnancy, a female can also be exposed to teratogens from the contaminated clothing or toxins within the seminal fluid of a partner. An additional study found that of 200 individuals referred for genetic counseling for a teratogenic exposure, 52% were exposed to more than one potential teratogen.

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.

HPE is not a condition in which the brain deteriorates over time. Although serious seizure disorders, autonomic dysfunction, complicated endocrine disorders and other life-threatening conditions may sometimes be associated with HPE, the mere presence of HPE does not mean that these serious problems will occur or develop over time without any previous indication or warning. These abnormalities are usually recognized shortly after birth or early in life and only occur if areas of the brain controlling those functions are fused, malformed or absent.

Prognosis is dependent upon the degree of fusion and malformation of the brain, as well as other health complications that may be present.

The more severe forms of encephalopathy are usually fatal. This disorder consists of a spectrum of defects, malformations and associated abnormalities. Disability is based upon the degree in which the brain is affected. Moderate to severe defects may cause mental retardation, spastic quadriparesis, athetoid movements, endocrine disorders, epilepsy and other serious conditions; mild brain defects may only cause learning or behavior problems with few motor impairments.

Seizures may develop over time with the highest risk before 2 years of age and the onset of puberty. Most are managed with one medication or a combination of medications. Typically, seizures that are difficult to control appear soon after birth, requiring more aggressive medication combinations/doses.

Most children with HPE are at risk of having elevated blood sodium levels during moderate-severe illnesses, that alter fluid intake/output, even if they have no previous diagnosis of diabetes insipidus or hypernatremia.

Otocephaly (from the Greek words "οτο", meaning “ear”, and "κεφάλη", meaning "head") is a type of head disorder (cephalic disorder).

This is a lethal condition in which the primary feature is the total or virtual absence of the lower jaw (a developmental anomaly called agnathia). The “oto” in the name refers to the relationship of the ears to the face in this disorder.

The condition is considered lethal because of a poorly functioning airway.

In otocephaly, agnathia may occur alone or together with holoprosencephaly.

It can be detected by the naked eye as well as dental or skull X-Ray testing.

The inheritance of Impossible syndrome is suspected to be autosomal recessive, which means the affected gene is located on an autosome, and two copies of the gene - one from each parent - are required to have an infant with the disorder.

3C syndrome, also known as CCC dysplasia, Craniocerebellocardiac dysplasia or Ritscher–Schinzel syndrome, is a rare condition, whose symptoms include heart defects, cerebellar hypoplasia, and cranial dysmorphism. It was first described in the medical literature in 1987 by Ritscher and Schinzel, for whom the disorder is sometimes named.

Currently, research is focusing on identifying the role of the genes on 18p in causing the signs and symptoms associated with deletions of 18p. This will ultimately enable predictive genotyping.

TGIF-Mutations and deletions of this gene have been associated with holoprosencephaly. Penetrance is incomplete, meaning that a deletion of one copy of this gene is not in and of itself sufficient to cause holoprosencephaly. Ten to fifteen percent of people with 18p- have holoprosencephaly, suggesting that other genetic and environmental facts play a role in the etiology of holoprosencephaly in these individuals.

Roberts syndrome is an extremely rare condition that only affects about 150 reported individuals. Although there have been only about 150 reported cases, the affected group is quite diverse and spread worldwide. Parental consanguinity (parents are closely related) is common with this genetic disorder. The frequency of Roberts syndrome carriers is unknown.