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.

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

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.

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.

Ring chromosome 14 syndrome is extremely rare, the true rate of occurrence is unknown (as it is "less than" 1 per 1,000,000), but there are at least 50 documented cases in the literature.

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.

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.

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.

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.

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

It can be associated with "ERCC6".

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.

It is supposed to be caused by defects of genes on chromosome 3 and 18. One form of Seckel syndrome can be caused by mutation in the gene encoding the ataxia telangiectasia and Rad3 related protein () which maps to chromosome 3q22.1-q24. This gene is central in the cell's DNA damage response and repair mechanism.

Types include:

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 rare cases that have been examined are often within families, or the people that have cases of micro syndrome have a mutation in their genes.

It can be associated with "RAB3GAP".

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).

There is no specific treatment for micro syndrome, but there are ways to help the disorders, and illnesses that come with it. Many individuals with Micro Syndrome need permanent assistance from their disorders and inabilities to move and support themselves. Seizures are not uncommon and patients should get therapy to help control them, and many patients also require wheelchairs to move, so an assistant would be needed at all times.

Those with micro syndrome are born appearing normal. At the age of one, mental and physical delays become apparent, along with some limb spasms. By the age of eight micro syndrome has already set in, and the patient will have joint contractures, Ocular Atrophy will become noticeable, the patient will most likely lose ability to walk, speak, and sometimes move at all.

A review from 2000 stated that life expectancy was reduced because of a tendency to develop cancer relatively early as well as deaths due to infections related to immunodeficiency.

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.

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.

Kaufman oculocerebrofacial syndrome is an autosomal recessive congenital disorder characterized by mental retardation, brachycephaly, upslanting palpebral fissures, eye abnormalities, and highly arched palate. It was characterized in 1971; eight cases had been identified as of 1995.

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

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.

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.

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

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.