Nutrition disorders and nutritional deficits may cause neurodevelopmental disorders, such as spina bifida, and the rarely occurring anencephaly, both of which are neural tube defects with malformation and dysfunction of the nervous system and its supporting structures, leading to serious physical disability and emotional sequelae. The most common nutritional cause of neural tube defects is folic acid deficiency in the mother, a B vitamin usually found in fruits, vegetables, whole grains, and milk products. (Neural tube defects are also caused by medications and other environmental causes, many of which interfere with folate metabolism, thus they are considered to have multifactorial causes.) Another deficiency, iodine deficiency, produces a spectrum of neurodevelopmental disorders ranging from mild emotional disturbance to severe mental retardation. (see also cretinism)

Excesses in both maternal and infant diets may cause disorders as well, with foods or food supplements proving toxic in large amounts. For instance in 1973 K.L. Jones and D.W. Smith of the University of Washington Medical School in Seattle found a pattern of "craniofacial, limb, and cardiovascular defects associated with prenatal onset growth deficiency and developmental delay" in children of alcoholic mothers, now called fetal alcohol syndrome, It has significant symptom overlap with several other entirely unrelated neurodevelopmental disorders. It has been discovered that iron supplementation in baby formula can be linked to lowered I.Q. and other neurodevelopmental delays.

Systemic infections can result in neurodevelopmental consequences, when they occur in infancy and childhood of humans, but would not be called a primary neurodevelopmental disorder per se, as for example HIV Infections of the head and brain, like brain abscesses, meningitis or encephalitis have a high risk of causing neurodevelopmental problems and eventually a disorder. For example, measles can progress to subacute sclerosing panencephalitis.

A number of infectious diseases can be transmitted either congenitally (before or at birth), and can cause serious neurodevelopmental problems, as for example the viruses HSV, CMV, rubella (congenital rubella syndrome), Zika virus, or bacteria like "Treponema pallidum" in congenital syphilis, which may progress to neurosyphilis if it remains untreated. Protozoa like "Plasmodium" or "Toxoplasma" which can cause congenital toxoplasmosis with multiple cysts in the brain and other organs, leading to a variety of neurological deficits.

Some cases of schizophrenia may be related to congenital infections though the majority are of unknown causes.

The syndrome primarily affects young males. Preliminary studies suggest that prevalence may be 1.8 per 10,000 live male births. 50% of those affected do not live beyond 25 years of age, with deaths attributed to the impaired immune function.

Opitz G/BBB Syndrome is a rare genetic condition caused by one of two major types of mutations: MID1 mutation on the short (p) arm of the X chromosome or a mutation of the 22q11.2 gene on the 22nd chromosome. Since it is a genetic disease, it is an inherited condition. However, there is an extremely wide variability in how the disease presents itself.

In terms of prevention, several researchers strongly suggest prenatal testing for at-risk pregnancies if a MID1 mutation has been identified in a family member. Doctors can perform a fetal sex test through chromosome analysis and then screen the DNA for any mutations causing the disease. Knowing that a child may be born with Opitz G/BBB syndrome could help physicians prepare for the child’s needs and the family prepare emotionally. Furthermore, genetic counseling for young adults that are affected, are carriers or are at risk of carrying is strongly suggested, as well (Meroni, Opitz G/BBB syndrome, 2012). Current research suggests that the cause is genetic and no known environmental risk factors have been documented. The only education for prevention suggested is genetic testing for at-risk young adults when a mutation is found or suspected in a family member.

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.

Lujan–Fryns syndrome is a rare X-linked dominant syndrome, and is therefore more common in males than females. Its prevalence within the general population has not yet been determined.

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

Alopecia contractures dwarfism mental retardation syndrome or (ACD mental retardation syndrome) is a developmental disorder which causes mainly baldness and dwarfism in combination with intellectual disability; skeletal anomalies, caries and nearsightedness are also typical.

The ACD mental retardation syndrome was first described in 1980 by Albert Schinzel and only few cases have since been identified in the world. At the time Dr. Schinzel made no conclusion of the hereditary pattern of this syndrome but similarities between cases reported by year 2000 seem to suggest autosomal or x-linked recessive inheritance or possibly a dominant mutation caused by mosaicism as causes of this syndrome.

X-linked intellectual disability (previously known as X-linked mental retardation) refers to forms of intellectual disability which are specifically associated with X-linked recessive inheritance.

As with most X-linked disorders, males are more heavily affected than females. Females with one affected X chromosome and one normal X chromosome tend to have milder symptoms.

Unlike many other types of intellectual disability, the genetics of these conditions are relatively well understood. It has been estimated there are ~200 genes involved in this syndrome; of these ~100 have been identified.

X-linked intellectual disability accounts for ~16% of all cases of intellectual disability in males.

As its name indicates, a person with the syndrome has one Y chromosome and four X chromosomes on the 23rd pair, thus having 49 chromosomes rather than the normal 46. As with most categories of aneuploidy disorders, 49,XXXXY syndrome is often accompanied by intellectual disability. It can be considered a form of 47, XXY Klinefelter syndrome, or a variant of it.

It is genetic but not hereditary. This means that while the genes of the parents cause the syndrome, there is a small chance of more than one child having the syndrome. The probability of inheriting the disease is about 1%.

The individuals with this syndrome are males, but 49, XXXXX also exists with similar characteristics.

Mental retardation and microcephaly with pontine and cerebellar hypoplasia (MICPCH), also known as Mental retardation, X-linked, syndromic, Najm type (MRXSNA), is a rare genetic disorder of infants characterised by intellectual disability and pontocerebellar hypoplasia.

The disorder is associated with a mutation in the "CASK" gene which is transmitted in an X-linked manner. As with the vast majority of genetic disorders, there is no known cure to MICPCH.

The following values seem to be aberrant in children with CASK gene defects: lactate, pyruvate, 2-ketoglutarate, adipic acid and suberic acid, which seems to backup the proposal that CASK affects mitochondrial function. It is also speculated that phosphoinositide 3-kinase in the inositol metabolism is impacted in the disease, causing folic acid metabolization problems.

Several X-linked syndromes include intellectual disability as part of the presentation. These include:

- Coffin–Lowry syndrome

- MASA syndrome

- MECP2 duplication syndrome

- X-linked alpha thalassemia mental retardation syndrome

- mental retardation and microcephaly with pontine and cerebellar hypoplasia

Since the symptoms caused by this disease are present at birth, there is no “cure.” The best cure that scientists are researching is awareness and genetic testing to determine risk factors and increase knowledgeable family planning. Prevention is the only option at this point in time for a cure.

M2DS is one of the several types of X-linked intellectual disability. The cause of M2DS is a duplication of the MECP2 or Methyl CpG binding protein 2 gene located on the X chromosome (Xq28). The MeCP2 protein plays a pivotal role in regulating brain function. Increased levels of MECP2 protein results in abnormal neural function and impaired immune system. Mutations in the MECP2 gene are also commonly associated with Rett syndrome in females. Advances in genetic testing and more widespread use of Array Comparative Genomic Hybridization has led to increased diagnosis of MECP2 duplication syndrome. It is thought to represent ~1% of X-linked male mental disability cases.

Treatment with isotretinoin may induce substantial resolution of skin lesions, but the risk of secondary infection remains.

Some people may have some mental slowness, but children with this condition often have good social skills. Some males may have problems with fertility.

The prognosis varies widely from case to case, depending on the severity of the symptoms. However, almost all people reported with Aicardi syndrome to date have experienced developmental delay of a significant degree, typically resulting in mild to moderate to profound intellectual disability. The age range of the individuals reported with Aicardi syndrome is from birth to the mid 40s.

There is no cure for this syndrome.

Unlike Borjeson-Forssman-Lehmann syndrome, a disorder that was determined to be very similar to WTS, the individuals with Wilson–Turner syndrome do not develop cataracts or hypermetropia later in life. By far, the most debilitating part of this disorder is intellectual disability. Many of the other symptoms are more easily managed through hormone treatment, proper diet and exercise, and speech therapy.

The aneuploidy is thought to be caused by problems occurring during meiosis, either in the mother or in both the mother and father. Successive nondisjunctions have been observed in the mother of at least one patient.

The features of the syndrome likely arise due to failure of X-inactivation and the presence of multiple X chromosomes from the same parent causing problems with parental imprinting. In theory, X-inactivation should occur and leave only one X chromosome active in each cell. However, failure of this process has been observed in one individual studied. The reason for this is thought to be the presence of an unusually large, and imbalanced, number of X chromosomes interfering with the process.

Zamzam–Sheriff–Phillips syndrome is a rare autosomal recessive congenital disorder. It is characterized by aniridia, ectopia lentis, abnormal upper incisors and intellectual disability. Not a lot of research has been undertaken of this particular disease so thus far there is no known gene that affects this condition. However it has been hypothesised that the symptoms described are found at a particular gene, though intellectual disability is believed to be due to a different genetic cause.

Consanguinuity (intermarrying among relatives such as cousins), often associated with autosomal recessive inheritance, has been attributed to the inheritance of this disease.

Gillespie syndrome, also called aniridia, cerebellar ataxia and mental deficiency. is a rare genetic disorder. The disorder is characterized by partial aniridia (meaning that part of the iris is missing), ataxia (motor and coordination problems), and, in most cases, intellectual disability. It is heterogeneous, inherited in either an autosomal dominant or autosomal recessive manner. Gillespie syndrome was first described by American ophthalmologist Fredrick Gillespie in 1965.

This disorder affects all demographics equally. The two families that were studied are of European ancestry. Wilson–Turner syndrome is considered to be a rare disease because it affects one individual out of one million.

The incidence rate of ATR-16 syndrome is not easy to estimate and it is thought to be underdiagnosed. Scientists have described more than 20 cases as of 2013.

Worldwide prevalence of Aicardi Syndrome is estimated at several thousand, with approximately 900 cases reported in the United States.

The syndrome is characterized by alopecia, hypogonadism, hypothyroidism, hearing loss, intellectual disability and diabetes mellitus. Electrocardiogram anomalies have also been reported.