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.

Microcephaly generally is due to the diminished size of the largest part of the human brain, the cerebral cortex, and the condition can arise during embryonic and fetal development due to insufficient neural stem cell proliferation, impaired or premature neurogenesis, the death of neural stem cells or neurons, or a combination of these factors. Research in animal models such as rodents has found many genes that are required for normal brain growth. For example, the Notch pathway genes regulate the balance between stem cell proliferation and neurogenesis in the stem cell layer known as the ventricular zone, and experimental mutations of many genes can cause microcephaly in mice, similar to human microcephaly. In addition, viruses such as cytomegalovirus (CMV) or Zika have been shown to infect and kill the primary stem cell of the brain—the radial glial cell, resulting in the loss of future daughter neurons. The severity of the condition may depend on the timing of infection during pregnancy.

In some cases, the defect is linked to mutations of the EMX2, SIX3, and Collagen, type IV, alpha 1 genes. Because having a sibling with schizencephaly has been statistically shown to increase risk of the disorder, it is possible that there is a heritable genetic component to the disease.

Vaccinating the majority of the population is effective at preventing congenital rubella syndrome.

The prognosis is poor; affected individuals are either stillborn or die shortly after birth. The longest survival reported in literature is of 134 days.

This syndrome is transmitted as an autosomal recessive disorder and there is a risk for recurrence of 25% in future pregnancies.

Microlissencephaly is listed in Orphanet database as a rare disease. There is no much information available about the epidemiology of microlissencepahly in literature. A PhD thesis has estimated the prevalence of microlissencepahly in South–Eastern Hungary between July 1992 and June 2006 to be a case every 91,000 live births (0.11:10,000).

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

Microhydranencephaly (MHAC) is a severe abnormality of brain development characterized by both microcephaly and hydranencephaly. Signs and symptoms may include severe microcephaly, scalp rugae (a series of ridges), and profound developmental delay. Familial occurrence of the condition is very rare but it has been reported in a few families. It has been suggested that MHAC is possibly inherited in an autosomal recessive manner.

Microlissencephaly (MLIS) is a rare congenital brain disorder that combines severe microcephaly (small head) with lissencephaly (smooth brain surface due to absent sulci and gyri). Microlissencephaly is a heterogeneous disorder i.e. it has many different causes and a variable clinical course. Microlissencephaly is a malformation of cortical development (MCD) that occurs due to failure of neuronal migration between the third and fifth month of gestation as well as stem cell population abnormalities. Numerous genes have been found to be associated with microlissencephaly, however, the pathophysiology is still not completely understood.

The combination of lissencephaly with severe congenital microcephaly is designated as microlissencephaly only when the cortex is abnormally thick. If such combination exists with a normal cortical thickness (2.5 to 3 mm), it is known as "microcephaly with simplified gyral pattern" (MSGP). Both MLIS and MSGP have a much more severe clinical course than microcephaly alone. They are inherited in autosomal recessive manner. Prior to 2000, the term “microlissencephaly” was used to designate both MLIS and MSGP.

Autosomal dominant porencephaly type I is rare and its prevalence and incidence are unknown. It affects males and females equally.

This disorder is caused by an abnormality of the TBCE gene, the locus for which is on Chromosome 1q42.3. The locus is a 230 kb region of gene with identified deletions and mutations in affected individuals. There are rare cases of the disorder not being due to a TBCE gene abnormality.

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."

Researchers are also investigating the genetic similarities between Dubowitz Syndrome and Smith-Lemli-Opitz syndrome (SLOS). Patients with SLOS and Dubowitz syndromes experience many of the same abnormalities, and the two disorders are hypothesized to be linked. A characteristic of SLOS is a low cholesterol level and a high 7-dehydrocholesterol level. Cholesterol is essential for several key functions of the body, including cell membrane structure, embryogenesis, and steroid and sex hormone synthesis. Impaired cholesterol biosynthesis or transport possibly accounts for most of the symptoms of both SLOS and Dubowitz. Although only a few patients with Dubowitz Syndrome have been identified with altered cholesterol levels, researchers are exploring whether Dubowitz Syndrome, like SLOS, carries a link to a defect in the cholesterol biosynthetic pathway.

The exact biochemical pathology of the disease is still under research because of the low prevalence of the disease and the wide array of symptoms associated with it. Several studies have focused on different aspects of the disease to try to find its exact cause and expression. One study examined the specific oral features in one patient. Another found abnormalities in the brain, such as corpus callosum dysgenesis, an underdeveloped anterior pituitary and a brain stalk with an ectopic neurohypophysis.

In at least some case, the gene lesion involves a mutation in the "CSB" gene.

It can be associated with "ERCC6".

Nicolaides–Baraitser syndrome (NCBRS) is a rare genetic condition caused by de novo missense mutations in the SMARCA2 gene and has only been reported in less than 100 cases worldwide. NCBRS is a distinct condition and well recognizable once the symptoms have been identified.

Although the exact pathology of Dubowitz syndrome is not known yet, it is heritable and classified as an autosomal recessive disease. Furthermore, there is an occasional parental consanguinity. Several cases point to Dubowitz syndrome occurring in monozygotic twins, siblings, and cousins. There is considerable phenotypic variability between cases, especially in regards to intelligence. Although substantial evidence points to the genetic basis of this disorder, the phenotypic similarity is found in fetal alcohol syndrome. Further studies need to be done to determine whether this environmental agent effects the expression of the genotype. Breakdown of chromosomes is known to occur.

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.

The Seckel syndrome or microcephalic primordial dwarfism (also known as bird-headed dwarfism, Harper's syndrome, Virchow-Seckel dwarfism, and Bird-headed dwarf of Seckel) is an extremely rare congenital nanosomic disorder.

Inheritance is autosomal recessive.

It is characterized by intrauterine growth retardation and postnatal dwarfism with a small head, narrow bird-like face with a beak-like nose, large eyes with down-slanting palpebral fissures , receding mandible and intellectual disability.

A mouse model has been developed. This mouse model is characterized by a severe deficiency of ATR protein. These mice suffer high levels of replicative stress and DNA damage. Adult Seckel mice display accelerated aging. These findings are consistent with the DNA damage theory of aging.

There is no known definitive single mechanism that causes colpocephaly. However, researchers believe there are many possible causes of colpocephaly. It is a common symptom of other neurological disorders in newborns, can be caused as a result of shunt treatment of hydrocephalus, developmental disorders in premature infants, due to intrauterine disturbances during pregnancy, genetic disorders, underdevelopment or lack of white matter in the cerebrum, and exposure of the mother and the developing fetus to medications, infections, radiation, or toxic substances. Also, it is usually more common in premature infants than in full-term infants, especially in babies born with hypoxia or lung immaturity.

Some of the central nervous system disorders which are associated with colpocephaly are as follows:

- polymicrogyria

- Periventricular leukomalacia (PVL)

- intraventricular hemorrhage

- Hydrocephalus

- schizencephaly

- microgyria

- microcephaly

- Pierre-Robin syndrome

- Neurofibromatosis

Often colpocephaly occurs as a result of hydrocephalus. Hydrocephalus is the accumulation of cerebrospinal fluid (CSF) in the ventricles or in the subarachnoid space over the brain. The increased pressure due to this condition dilates occipital horns causing colpocephaly.

The most generally accepted theory is that of neuronal migration disorders occurring during the second to fifth months of fetal life. Neuronal migration disorders are caused by abnormal migration, proliferation, and organization of neurons during early brain development. During the seventh week of gestation, neurons start proliferating in the germinal matrix which is located in the subependymal layer of the walls of the lateral ventricles. During the eighth week of gestation, the neurons then start migrating from the germinal zone to cortex along specialized radial glial fibers. Next, neurons organize themselves into layers and form synaptic contacts with other neurons present in the cortex. Under normal conditions, the neurons forming a germinal layer around ventricles migrate to the surface of the brain and form the cerebral cortex and basal ganglia. If this process is abnormal or disturbed it could result in the enlargement of the occipital horns of the lateral ventricles. Common prenatal disturbances that have been shown to disturb the neuronal migration process include the following:

- continuation of oral contraceptives

- exposure to alcohol

- intrauterine malnutrition

- intrauterine infections such as toxoplasmosis

- maternal drug ingestion during early pregnancy such as corticosteroids, salbutamol, and theophylline

Researchers also believe that these factors can cause destruction of neural elements that have previously been normally formed.

It is suggested that the underdevelopment or lack of white matter in the developing fetus could be a cause of colpocephaly. The partial or complete absence of white matter, also known as agenesis of the corpus callosum results in anatomic malformations that can lead to colpocephaly. This starts to occur around the middle of the second month to the fifth month of pregnancy. The lateral ventricles are formed as large cavities of the telencephalic vesicle. The size of the ventricles are decreased in normal development after the formation of the Foramen of Magendie, which decompresses the ventricular cavities. Myelination of the ventricular walls and association fibers of the corpus callosum and the calcarine fissure helps shape the occipital horns. In cases where this developmental process is interrupted, occipital horns are disproportionately enlarged.

Colpocephaly has been associated with chromosomal abnormalities such as trisomy 8 mosaic and trisomy 9 mosaic. A few reports of genetically transmitted colpocephaly are also found in literature. Some of these are of two siblings, monozygotic twins, and non-identical twins. The authors suggest a genetic origin with an autosomal or X-linked recessive inheritance rather than resulting from early prenatal disturbances.

DeSanctis–Cacchione syndrome is an extremely rare disorder characterized by the skin and eye symptoms of xeroderma pigmentosum (XP) occurring in association with microcephaly, progressive mental retardation, retarded growth and sexual development, deafness, choreoathetosis, ataxia and quadriparesis.

The classic triad for congenital rubella syndrome is:

- Sensorineural deafness (58% of patients)

- Eye abnormalities—especially retinopathy, cataract, and microphthalmia (43% of patients)

- Congenital heart disease—especially pulmonary artery stenosis and patent ductus arteriosus (50% of patients)

Other manifestations of CRS may include:

- Spleen, liver, or bone marrow problems (some of which may disappear shortly after birth)

- Intellectual disability

- Small head size (microcephaly)

- Eye defects

- Low birth weight

- Thrombocytopenic purpura

- Extramedullary hematopoiesis (presents as a characteristic blueberry muffin rash)

- Hepatomegaly

- Micrognathia

Children who have been exposed to rubella in the womb should also be watched closely as they age for any indication of:

- Developmental delay

- Autism

- Schizophrenia

- Growth retardation

- Learning disabilities

- Diabetes mellitus

- Glaucoma

Al-Raqad syndrome (ARS) is a congenital autosomal recessive syndrome discovered by Jordanian physician Mohammad Al-Raqad.

It's characterized by:

- microcephaly

- growth delay

- Psycho-motor developmental delay

- congenital hypotonia.

Al-Raqad syndrome is caused by mutation of DCPS gene.

Neu–Laxova syndrome (also known as Neu syndrome or Neu-Povysilová syndrome, abbreviated as NLS) is a rare autosomal recessive disorder characterized by severe intrauterine growth restriction and multiple congenital malformations. Neu–Laxova syndrome is a very severe disorder, leading to stillbirth or neonatal death. It was first described by Dr. Richard Neu in 1971 and Dr. Renata Laxova in 1972 as a lethal disorder in siblings with multiple malformations. Neu–Laxova syndrome is an extremely rare disorder with less than 100 cases reported in medical literature.

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.

The cause of this condition is apparently due to mutation in the UBE3B gene and is inherited via autosomal recessive manner. This gene is located at molecular location- base pairs 109,477,410 to 109,543,628 and position 24.11 on chromosome 12.