Microcephaly: A clinical genetics approach

INTRODUCTION — Microcephaly is an important neurologic finding. Deviations from normal head growth may be the first indication of an underlying congenital, genetic, or acquired problem. Many genetic conditions are associated with an abnormal pattern of head growth; the earlier these conditions are detected, the earlier appropriate treatment, services, and genetic counseling can be provided [1].

A clinical genetics approach to microcephaly in infants and children will be presented here. At the heart of this approach is an attempt in each case to formulate an etiologic diagnosis that gives at least an indication of the sibling recurrence risk. The etiology and primary care evaluation of microcephaly in infants and children and microcephaly related to Zika virus are discussed separately. (See "Microcephaly in infants and children: Etiology and evaluation" and "Zika virus infection: An overview", section on 'Children'.)

DEFINITION — The definition of microcephaly is not standardized. It is sometimes defined as an occipitofrontal circumference (OFC) more than three standard deviations (SDs) below the mean for a given age, sex, and gestation. Other times, it is defined as an OFC more than two SDs below the appropriate mean (ie, less than the 3^rd percentile).

OFC measurements at birth are necessary to establish a diagnosis of primary microcephaly. (See 'Primary genetic microcephaly and its syndromes' below.)

It can be difficult to measure OFC accurately in children with severe microcephaly without the landmark of the occiput. It is important to record measurements rather than percentiles, as head circumference charts vary, especially up to the age of three years. Use the most recent culturally and ethnically relevant charts to determine percentiles [2].

If microcephaly is defined as a head size less than three SDs below the appropriate mean, it is more likely to be associated with genetic and nongenetic disorders affecting brain development. In contrast, if microcephaly is defined as more than two SDs below the mean, many individuals without disorders affecting brain growth will be included. Among children whose head circumference is between two and three SDs below the appropriate mean, the yield of identifying a disorder affecting brain development may be increased if the height or length is greater than the 50^th percentile for age and sex.

Whatever definition is employed, measurement and appropriate charting of OFC is part of the evaluation of individuals who have a developmental delay, learning disability, or intellectual disability. Population-based studies indicate that it is important to measure OFC in all infants when height and weight are measured, because reduced head circumference growth in early life is associated with diminished cognitive abilities thereafter [3-6]. (See "Specific learning disorders in children: Role of the primary care provider", section on 'Medical evaluation' and "Intellectual disability (ID) in children: Clinical features, evaluation, and diagnosis", section on 'Clinical evaluation'.)

TERMINOLOGY

●Secondary microcephaly – A descriptive term for genetic and nongenetic disorders in which the head growth slows after birth.

●Primary microcephaly – Primary microcephaly (also called congenital microcephaly) is present at birth. Most cases will be evident by 20 weeks of gestation. Primary microcephaly can be acquired (eg, due to cytomegalovirus) or genetic.

The term "primary microcephaly" was originally associated with one particular autosomal recessive microcephaly phenotype (microcephaly primary hereditary, MCPH) (picture 1) [7]. This phenotype is now known to be one of several primary genetic microcephalies, described below.

●Primary genetic microcephaly – The primary genetic microcephaly phenotype is clinically and genetically heterogeneous. Multiple gene loci (designated MCPH1, MCPH2, etc) have been identified, and more are yet to be discovered [8] or confirmed [9]. (See 'Primary genetic microcephaly and its syndromes' below.)

Primary genetic microcephalies are thought to result from failure to produce enough neurons during fetal development; however, MCPH proteins are expressed in postnatal cerebral neurons, so postnatal expression may also be a factor [10]. Defective production of neurons with secondary degeneration also may occur (eg, MCPH10, caused by homozygous mutation in ZNF335) [11].

Classic primary genetic microcephaly includes the following clinical features:

•Reduced occipitofrontal circumference (OFC) at birth, after which the degree of microcephaly (ie, standard deviation below expected) does not substantially change, leading to persistently reduced OFC in adulthood

•Relatively typical brain anatomy

•Relative absence of neurologic signs

•Nonprogressive mild, moderate, or severe learning difficulties

In primary genetic microcephaly syndromes with the exception of MCPH1, height, weight, and growth velocity are typically within the normal range. If height, weight, and growth velocity are substantially reduced, then a diagnosis other than primary genetic microcephaly, including Seckel syndrome, should be considered. However, the phenotypes of some MCPH syndromes and Seckel syndrome overlap. (See 'Primary genetic microcephaly and its syndromes' below.)

Autosomal recessive inheritance has also been recognized as a characteristic feature, and this has broadened the range of associated phenotypes beyond the original clinical description. For example, the following conditions are sometimes listed under the heading primary genetic microcephaly because they are inherited in an autosomal recessive fashion [12,13] (see 'Primary genetic microcephaly and its syndromes' below):

•Microcephaly with early onset epilepsy (MCSZ, MIM #613402)

•Amish microcephaly (MCPHA, MIM #607196)

•Microcephaly with or without other brain malformations caused by nonsense or missense mutations (MCPH2, MIM #604317)

•Microcephaly with simplified gyral pattern, cerebellar and/or brainstem hypoplasia (MIM %603802)

Genetic heterogeneity also bedevils orderly classification (eg, different mutations in the Amish microcephaly gene, SLC25A19, result in a metabolic disorder affecting the mitochondrial thiamine pyrophosphate carrier with a variable phenotype ranging from early, lethal Amish microcephaly to an adult condition with normal OFC/cognition, striatal necrosis, and polyneuropathy) [14].

●Postnatal onset microcephaly – Postnatal onset microcephaly is a term used to describe a brain that had normal or near-normal size antenatally (or if not measured antenatally, then at birth) and grows abnormally slowly thereafter. Acquired (eg, hypoxic ischaemia) and genetic disorders (eg, Angelman syndrome, phenylketonuria) can cause postnatal onset microcephaly. Postnatal microcephaly may go undiagnosed, due to lack of or mismeasurement.

The term "postnatal onset microcephaly" is preferred to "secondary microcephaly" because "secondary microcephaly" may have multiple interpretations (eg, nongenetic or acquired as well as head growth that slows after birth).

●"Benign" familial microcephaly – "Benign" familial microcephaly occurs in children with an OFC two to four standard deviations below the mean, with a neurologically normal parent with a similar-sized head (although in KIF11-dominant primary microcephaly, OFC may normalize in adulthood), and negative evaluation for other causes, particularly treatable inborn errors of metabolism. (See 'Uncertain diagnosis' below.)

Children with benign familial microcephaly have no neurologic signs. Whether associated mild learning or intellectual disability is unrelated or related to variable penetrance of a genetic disorder is a matter of debate. Associated moderate/severe learning or intellectual disability should prompt genomic analysis. (See 'Microcephaly with prominent neurologic abnormalities' below.)

●Relative microcephaly – "Relative microcephaly" is a shorthand expression that usually is used to describe the child with neurologic impairments who has reduced head circumference relative to their somatic size, or relative to the head circumferences of their parents without neurologic impairments (figure 1). The term is best avoided.

INITIAL GENETICS CONSULTATION — The objective of genetics consultation for a family with a child or relative affected by microcephaly is to formulate a diagnosis (eg, primary, syndromic, metabolic) and to estimate the chance of recurrence of the condition in another child. The clinical geneticist must distinguish syndromic from nonsyndromic microcephaly. They should collaborate with colleagues to diagnose metabolic and neurologic conditions amenable to disease modification therapy (eg, the ketogenic diet in children with glucose carrier transport deficiency caused by variants in GLUT1) that may cause microcephaly.

At first consultation, it is uncommon for the geneticist to make a confident diagnosis of a specific condition, and additional evaluation generally is necessary [15-18]. The subsequent clinical and laboratory evaluation are best determined on a case-by-case basis. Factors to be considered include the onset of microcephaly, associated dysmorphism or congenital anomalies, maternal/environmental factors, and progressive neurologic abnormalities [2].

History — A comprehensive approach to history-taking, including the family history, and clinical examination of the child with microcephaly are described separately. (See "Microcephaly in infants and children: Etiology and evaluation", section on 'Postnatal evaluation'.)

Points worth highlighting include:

●The age at which microcephaly was first observed; occipitofrontal circumference (OFC) must be measured at birth to establish a diagnosis of primary microcephaly (see 'Primary genetic microcephaly and its syndromes' below)

●History of antenatal insult or maternal illness, such as cytomegalovirus [19]

●Fetal exposures, including alcohol, drugs (eg, antiseizure medications), infections (eg, cytomegalovirus or Zika virus), and toxins (eg, undiagnosed maternal hyperphenylalaninemia [20,21]) (see "Zika virus infection: An overview", section on 'Children')

●Whether other relatives are affected

●Parental consanguinity

●Developmental history

Several consultations, a trusting clinician-patient relationship, and tact often are required to assess factors such as prenatal infection, maternal drug and medication use, maternal alcohol consumption, or the intellectual attainments of parents and relatives. (See "Fetal alcohol spectrum disorder: Clinical features and diagnosis", section on 'Prenatal alcohol exposure'.)

Examination — Physical examination should include an assessment of the genetic contribution to microcephaly by measuring the parents' OFC and plotting these measurements on head circumference charts appropriate for sex (usually plotted for the age 18 or 21 values). A head circumference reference chart for birth to 21 years was published in the United States in 2010 [22]. For direct comparison, simultaneously plot the OFC measurements of the child, parents, and any siblings on such a chart (figure 1). For most neurologically normal children, when the head sizes of the parents and the child are plotted and compared, the child's OFC lies between the standard deviation (SD) or centile plots of both parents, just as the midparental height is a guide to the expected height of a child. Although the Weaver curve [23] achieves the same goal with greater precision, it takes a little longer to complete. (See "Microcephaly in infants and children: Etiology and evaluation", section on 'Parental OFC and Weaver curve'.)

Full neurologic examination should occur, including assessment of the skin, hair, and nails and evaluation for dysmorphism and motor disorders.

Laboratory evaluation — The laboratory evaluation is best determined on a case-by-case basis, bearing in mind that the objective is to formulate a diagnosis and estimate the chance of recurrence of the condition in another child. If there is a suspicion of a metabolic cause for microcephaly or no other etiology identified, appropriate referral to the metabolic service should be made at an early stage in case there is an underlying, treatable inborn error of metabolism. (See 'Metabolic microcephaly' below.)

If viral-induced microcephaly is suspected, appropriate testing should be undertaken. (See "Microcephaly in infants and children: Etiology and evaluation", section on 'Postnatal evaluation'.)

Chromosome studies are important in all cases. Array comparative genomic hybridization (CGH, and sometimes known as a "microarray") studies have replaced traditional cytogenetic tests as the first-line genetic test in children with neurodevelopmental disorders, particularly when there is less severe microcephaly, malformation, or dysmorphism. Array CGH has a higher abnormality detection rate than traditional cytogenetic studies, and this increased resolution permits detection of much smaller chromosomal deletions and duplications, sometimes even at the gene and exon level (eg, homozygous microcephalin [MCPH1] deletions) [24-26]. Traditional cytogenetic studies, but not microarrays, can detect abnormal, prophase-like cells suggesting primary microcephaly due to mutations in MCPH1 and MSI1 genes, but, overall, these are very rare causes of primary microcephaly. Genomic sequencing is discussed below. (See 'Array comparative genomic hybridization' below.)

Neuroimaging — Neuroimaging may be warranted after microarray and/or targeted testing. Although neuroimaging has a low yield compared with wider genomic sequencing, it may identify an acquired pattern of brain injury. When there is a request for accurate genetic counseling, magnetic resonance imaging (MRI) of the brain may be undertaken, despite the requirement for sedation or general anesthesia in young or uncooperative individuals. Neonates can be more easily scanned when sleeping, avoiding the need for anesthesia; however, more minor structural brain anomalies may be overlooked. Simplified gyral folding, sometimes suggestive of lissencephaly, is seen in the majority of cases with severe microcephaly. Simultaneous magnetic resonance spectroscopy may be warranted if rare neurometabolic causes of microcephaly are suspected (eg, brain creatine deficiency syndromes) [27]

Categorization after initial consultation — After the initial genetics assessment, most children with microcephaly can be assigned to one of the following broad clinical categories, although some patients have features of more than one category:

●Microcephaly (OFC -2 to -4 SDs) with an undiagnosed pattern of dysmorphism – In such children, it is important to rule out chromosomal defects, specific dysmorphic syndromes, and environmental factors such as prenatal alcohol exposure. For children in this category, learning difficulties rather than microcephaly is the significant finding. This category usually has a lower empiric risk of recurrence, except in families where one parent is likely affected. (See 'Microcephaly with dysmorphism' below.)

●Primary microcephaly phenotype (OFC -4 to -11 SDs) – Classic cases of primary microcephaly have minimal dysmorphism and normal neurologic examination (although the face may appear abnormal due to the abnormal ratio between the face and the cranial vault). This category generally has a high risk of recurrence because the primary microcephaly phenotype is usually due to an autosomal recessive condition. A dominant form of primary microcephaly has now been reliably described, often with little effect on learning abilities (see 'Uncertain diagnosis' below). Note that the phenotype is not always classic; in such cases brain MRI findings may help to identify a particular type of genetic microcephaly. (See 'Neuroimaging' above and 'Primary genetic microcephaly and its syndromes' below.)

●Microcephaly with prominent neurologic abnormalities (OFC -2 to -4 SDs) – This category frequently includes postnatal reduction in brain growth with dystonia/spasticity, global developmental impairments, seizures including epileptic encephalopathy, and diverse brain MRI abnormalities. These may include an admixture of recessive disorders including metabolic conditions, new dominant mutations (especially in some, but not all, cases with early infantile epileptic encephalopathy), and, occasionally, difficult-to-identify adverse prenatal events. The recurrence risk varies from one in four to zero, hence the importance of making a definite diagnosis. (See 'Microcephaly with prominent neurologic abnormalities' below.)

SUBSEQUENT GENETICS ASSESSMENT — The initial genetic assessment may result in the patient being assigned informally to one of the broad categories described in the previous section (see 'Categorization after initial consultation' above). Thereafter, the need for further laboratory investigations is driven by consultations with colleagues – specialists in metabolism, pediatric neurology, and neuroradiology – and by the desire of parents to have more information on recurrence risks and options for future pregnancies.

Microcephaly with dysmorphism — Microcephaly with dysmorphism is a common scenario in the genetic clinic (noting the above caveat of the pseudoabnormal appearance of the face in children with significant microcephaly related to the abnormal ratio between the face and cranial vault). (See 'Categorization after initial consultation' above.)

The occipitofrontal circumference (OFC) at birth may be normal or mildly reduced. Subsequently, the OFC may follow a trajectory between two and four standard deviations (SDs) below the mean for age, sex, and gestational age. Decreased head circumference may be noted at the child's first presentation with developmental impairments. Developmental impairments often are global, but the severity across domains (eg, motor, language) is not necessarily uniform. Other clinical problems, such as organ malformation, visual impairments, or hearing loss, can lead to an earlier presentation. The risk of recurrence depends upon the underlying diagnosis.

Genetic assessment is vital when seeking an underlying syndrome. Sometimes, a subtle pattern of dysmorphisms suggests a "gestalt" diagnosis (ie, a pattern that is easily recognized), such as Angelman syndrome, Rubinstein-Taybi syndrome, or Cornelia de Lange syndrome types 1 through 5 (MIM #122470, MIM #300590, MIM #610759, MIM#614701, MIM #300882).

Williams and Angelman syndromes are two relatively common conditions, with well-defined molecular genetic pathologies on chromosome 7 and chromosome 15, respectively, that cause mildly reduced head circumference. Such well-known syndromes increasingly act as clinical cornerstones for development of new knowledge. As an example, recognition of the clinical overlap between Rett and Angelman syndrome preceded the expanding spectrum of Angelman syndrome-like and Rett syndrome-like conditions, with various combinations of severe learning difficulties, epilepsy, movement disorder or ataxia, irregular breathing, and reduced OFC (table 1) [28-33]. The phenotypes of affected adults with less familiar gestalt conditions are now being explored as a result of easier molecular diagnostic confirmation with new deoxyribonucleic acid (DNA) sequencing technologies [34]. (See 'Genetic testing' below.)

Rarely, the phenotype of a dysmorphic infant is so striking that diagnosis readily follows. A good example is the autosomal recessive microcephaly-capillary malformation syndrome due to mutations in STAMBP [35]. More often, however, there is no firm clinical diagnosis. Difficulties arise in cases where the clinical evidence is weak or just suggestive. In some cases, family history is crucial (eg, consanguinity, ethnic background, affected relatives). Confirmed information from the family history may be the only evidence for reliable diagnosis of a hitherto unknown autosomal dominant, recessive, or X-chromosome-linked microcephaly syndrome.

Evaluation by a geneticist is also important to assess less common clinical signs such as body asymmetries, pigmentary rash along Blaschko lines (linear streaks on limbs and whorled patterns around the trunk (figure 2)), and unusual dysmorphisms (eg, affecting the digits in diploid/triploid mosaicism (picture 2) or the hairline in tetrasomy 12p [Pallister-Killian syndrome]). These signs indicate mosaic genetic abnormalities that may be identified through cytogenetic studies on tissue samples (eg, skin or scrapings from the buccal mucosa).

If the pattern of dysmorphisms and other clinical signs does not suggest a diagnosis, which commonly happens, the clinician is faced with the challenge of scrutinizing hundreds of case reports seeking evidence for a specific microcephaly syndrome [36]. This process requires:

●Detailed examination by a clinical dysmorphologist to identify the obvious and not-so-obvious clinical features

●Interrogation of computerized syndrome and medical publication databases for candidate diagnoses featuring one, a few, or any combination of the noted clinical features

●Discussion of cases with experienced colleagues at clinical dysmorphology meetings, especially when there are clues of uncertain clinical significance

The computerized database provides a list of diagnoses that should be considered. However, the dysmorphologist must decide which of the candidate diagnoses are more plausible in the patient. This judgment requires extensive clinical experience. In one child, the presence of a "hard" diagnostic finding, such as choanal atresia, may narrow the number of candidate diagnoses. However, in another child, the absence of choanal atresia does not necessarily exclude these same conditions. "Soft" features, such as ptosis, epicanthus, clinodactyly (picture 3), or single palmar crease (picture 4), are common and nonspecific (they may even be inherited and totally unrelated to the presenting complaint (picture 3)), but in certain combinations a "gestalt" diagnosis is suggested: The classic example is immediate recognition of Down syndrome, yet all genetics practitioners will have missed what is, with hindsight, such an obvious diagnosis. (See "Down syndrome: Clinical features and diagnosis", section on 'Dysmorphic features'.)

Primary genetic microcephaly and its syndromes — Characteristic clinical features of the classic primary genetic microcephaly phenotype include (picture 1):

●Reduced OFC at birth leading to greatly reduced OFC in adulthood

●Relatively typical brain anatomy

●Relative absence of neurologic signs

●Nonprogressive mild, moderate, or (less commonly) severe learning difficulties

However, the classic primary microcephaly phenotype is not as pure or homogeneous as was originally thought. The OFC is not always markedly reduced, brain architecture is not always normal, and spasticity and seizures are not always absent [8,37-40]. The MCPH1 and MSI1 phenotypes include short stature and the cytogenetic finding of increased prophase-like cells (see 'Laboratory evaluation' above). The emerging biology of many primary microcephaly genes is that they control fundamental cell functions, including cell division and cell cycle checkpoints, DNA damage repair, and chromatin remodeling [41].

Despite expanding knowledge, what is known about the clinical genetics of primary microcephalies represents only a small proportion of the information necessary to provide accurate genetic counseling for all families who have a child with greatly reduced OFC for no apparent reason. In most such cases, there is a substantial empirical risk of recurrence in siblings [42,43], which seems mostly due to autosomal recessive gene mutations. Molecular genetic testing may facilitate identification of an underlying diagnosis. In the authors' experience, only one-half of children diagnosed with a primary microcephaly syndrome have a molecular etiology defined, although it is likely that the diagnosis rate will increase as new MCPH genes are discovered [44]. The introduction of next-generation sequencing, which allows simultaneous analysis of many/all MCPH genes, has lessened the difficulties of sequential testing. (See 'Second- or "next-generation" sequencing' below and 'Approach to molecular or DNA testing for microcephaly' below.)

From a clinical standpoint, when the OFC is more than four SDs below the appropriate mean with the classic primary microcephaly (MCPH) phenotype (ie, a child with severe microcephaly, relatively typical brain anatomy, and no other dysmorphic features; relative absence of neurologic signs; and nonprogressive, moderate learning difficulties), genetic analysis of ASPM (abnormal spindle-like, microcephaly associated, MIM *605481), the gene responsible for MCPH5 (MIM #608716), is most likely to detect mutations [45]. (See 'First-generation sequencing' below.)

After ASPM, the next most frequently encountered MCPH gene is probably WDR62 (WD repeat-containing protein 62, MIM *613583), the gene responsible for MCPH2 (MIM #604317). Mutations in WDR62, a spindle pole protein expressed in neuronal precursor cells undergoing mitosis in embryonic neuroepithelium, cause microcephaly with a structurally normal brain if the mutations are missense; with nonsense mutations, the phenotype is more severe and may involve a spectrum of cerebral malformations including lissencephaly, schizencephaly, polymicrogyria, heterotopias, and cerebellar abnormality [46,47]. Patients with WDR62 mutations frequently have asymmetry of cortical size and malformations [48].

Early onset and severe epilepsy is featured in the complex MCSZ phenotype (microcephaly, seizures, and variable cognitive impairment, MIM #613402) that was identified in affected patients from different ethnic backgrounds. Mutations in the gene for MCSZ (polynucleotide kinase 3'-phosphatase [PNKP, MIM *605610]) cause cellular sensitivity to radiation. The reporting of two additional cases expanded the MCSZ phenotype to include progressive polyneuropathy and cerebellar atrophy with less severe epilepsy [49].

Primary microcephaly syndromes that are associated with defective DNA repair include MCPH1 (MIM #251200) due to mutations in MCPH1 (also known as microcephalin and BRIT1) [50], Nijmegen breakage syndrome (MIM #251260), and ligase-4 syndrome (LIG4 syndrome, MIM #606593). LIG4 syndrome is very rare. Both Nijmegen breakage and LIG4 syndromes feature microcephaly with dysmorphisms, growth retardation, cellular radiosensitivity, and variable predispositions to immunodeficiency/malignancy, with relatively normal cognition in some cases. Chromosomal breakage studies demonstrating increased cellular sensitivity to ionizing radiation may still be the best screening test when investigating patients who are possibly affected by a DNA repair disorder, with negative genomic sequencing. (See "Nijmegen breakage syndrome".)

The contribution of recessive mutations in MSI1 causing primary microcephaly is yet to be fully defined. MSI1 controls messenger ribonucleic acid (mRNA) stability, including MCPH1 mRNA.

The autosomal recessive microcephaly primordial dwarfism syndromes are a group of unmistakable conditions that cause profound microcephaly with equally profound short stature [51]. The identified gene defects lie in fundamental cellular processes such as genome replication, DNA damage response, and centrosome function. In some rare cases, despite profoundly reduced OFC, there is normal cognition (eg, Bloom syndrome [MIM #210900]). Seckel syndrome (MIM #210600) is the archetypal phenotype, exhibiting extreme pre- and postnatal growth retardation, microcephaly, sloping forehead, prominent nose, and small chin. Seckel syndrome is usually due to recessive mutations in gene encoding ATR (ataxia telangiectasia and Rad3-related), a protein kinase that plays a central role in the DNA damage response pathway. A similar phenotype is caused by mutations in the gene encoding ATR-Interacting Protein (ATRIP), partner protein of ATR required for ATR stability and recruitment to the site of DNA damage [52]. Some individuals with CDK5RAP2 (MCPH3) and CPAP (MCPH6) mutations can have a Seckel syndrome phenotype. A milder version of the Seckel syndrome phenotype has been diagnosed in patients who have mutations in a primary microcephaly gene Cep152 (MCPH9) [53].

Clinically related to Seckel syndrome are microcephalic primordial dwarfism type II (MOPD II, MIM #210720) and Meier-Gorlin syndrome type 1 (MGORS1, MIM #224690) due to mutations in pericentrin (PCNT) and origin recognition complex 1 (ORC1), respectively. Underlying these syndromes are defective genetic processes for cilia formation, centrosome function, and DNA replication licensing [54]. Precise diagnosis of such conditions is important; otherwise, newly recognized and potentially treatable clinical complications such as Moya disease in MOPD II are unappreciated [55]. As another example, autosomal recessive insulin-like growth factor deficiency (MIM #608747) is a partially treatable cause of microcephaly, sensorineural deafness, and intellectual disability.

Microcephaly with prominent neurologic abnormalities — Children with microcephaly and neurologic abnormalities but with a typical appearance are affected by a wide range of static and degenerative disorders. Presentations are diverse, including delayed development or developmental regression, sensory impairments, seizures, movement disorders/ataxia, and acute coma or encephalopathy. In such patients, microcephaly may not be present at birth and the development of microcephaly in the first year leads to descriptions such as acquired, secondary, or postnatal. The risk of recurrence depends upon the underlying diagnosis.

Logical progression through a series of genomic, biochemical tests and brain imaging studies is required for diagnosis. MRI of the brain and genomic studies early in the evaluation are supplemented by metabolic studies. For chromosome investigations, array comparative genomic hybridization studies in parallel with genomic sequencing are the first choice, but conventional cytogenetic studies supplemented by fluorescence in situ hybridization examination may still be best to exclude the ring chromosome 20 syndrome, which causes epileptic regression in a child whose development may have been normal until the time of presentation [56]. (See 'Array comparative genomic hybridization' below and 'Traditional cytogenetic studies' below.)

Discussion with the neuroradiologist is critical when brain abnormalities are detected by MRI. More detailed classification of clinical-neuroradiologic phenotypes combined with genetic studies has led to identification of new brain development syndromes and greatly improved genetic advice for families [57,58]. As examples:

●The autosomal recessive, prenatal onset, neurodegenerative pontocerebellar hypoplasias are diagnosed by brain MRI findings. In more than one-half of carefully selected cases, gene mutations are identified in either transfer RNA splicing endonuclease subunit gene (TSEN54) or nuclear encoded mitochondrial arginyl transfer RNA synthetase gene (RARS2) [59,60].

●Microcephaly due to mutations in calcium/calmodulin-dependent serine protein kinase (CASK, MIM *300172), an X-linked gene. CASK mutations cause microcephaly, optic atrophy, pontine and cerebellar hypoplasia, and nystagmus in affected males (MICPCH syndrome, MIM #300749) [61,62]. Epilepsy is common. Heterozygous females can be severely affected with significant learning problems, an abnormal brain MRI, and postnatal microcephaly [63,64].

●Biallelic mutations were identified in ARFGEF2 in a syndrome of acquired microcephaly with nodular heterotopia, regression, dystonic quadriplegia, and obstructive cardiomyopathy [65].

●Profound microcephaly (OFC smaller than 10 SDs) with underlying microlissencephaly (MIM #614019) is caused by NDE1 biallelic mutations that lead to defective progress through mitosis, emphasizing that normal cerebral cortical neurogenesis is dependent on intact mitotic mechanisms, as exemplified in other primary microcephalies.

In the unexplained cases without clinical, laboratory, or neuroradiologic clues, there are a small number of autosomal recessive, nonsyndromic intellectual disability genes that might cause postnatal-onset microcephaly (eg, trafficking protein particle complex, subunit 9 [TRAPPC9, MIM *611966]) [66-68].

For the few cases with microcephaly and evidence pointing to environmental factors (eg, MRI features indicating vascular damage, cerebral destruction, or prenatal infection), there are some inherited mimics, including the not uncommon Aicardi-Goutières syndrome, that have high risk of recurrence (table 2) [69-79]. Identification of MSI1 MCPH led to the discovery of the critical role of MSI1 in embryonic/fetal Zika virus replication being confined to the central nervous system neural precursors, and presumably contributing to Zika microcephaly [80].

Metabolic microcephaly — Metabolic microcephaly usually develops postnatally. Although microcephaly is neither a sensitive nor specific indicator of inborn errors of metabolism, it is important not to miss a treatable metabolic disorder. A 2012 review identified over 80 treatable inborn errors of metabolism that can cause intellectual disability [81]. The authors of the review developed a tool to facilitate detection of these disorders. The tool is accessible online and on mobile devices (Treatable ID) [82].

Examples of metabolic microcephaly syndromes include:

●Maternal or infantile phenylketonuria – Among metabolic microcephaly syndromes, maternal phenylketonuria is the only condition that, when undiagnosed, has 100 percent chance of damaging the fetus, and yet it is uniquely preventable [20,21]. (See "Overview of phenylketonuria", section on 'Phenylalanine embryopathy (maternal PKU)'.)

●Adenylosuccinate lyase deficiency – Adenylosuccinate lyase deficiency (MIM #103050), a disorder of purine biosynthesis, is not treatable [83]. However, it may be underdiagnosed in its severe and attenuated forms because diagnosis requires specific examination of urinary purine metabolites.

●Cerebral glucose transporter deficiency – Cerebral glucose transporter (GLUT1) deficiency (MIM #606777) is a treatable condition with a variable phenotype [84,85]. Postnatal microcephaly and seizures are prominent features in the earliest presenting cases, but movement disorders with progressive neurologic signs and normal OFC are more likely in late presenting cases. Diagnosis of this autosomal dominant condition is most conveniently made by analysis of the SLC2A1 gene (MIM *138140). It can respond well to a ketogenic diet.

●Phosphoglycerate dehydrogenase deficiency – Phosphoglycerate dehydrogenase deficiency (MIM #601815) is an autosomal recessive disorder caused by a defect in the synthesis of L-serine. Congenital microcephaly, intractable seizures, and irritability are prominent in the first few months of life. White matter volume loss is evident on brain MRI, and spastic quadriplegia ensues. Treatment with serine lessens epilepsy severity and irritability but does not seem to improve psychomotor development. Not all cases are severely affected, highlighting the need to obtain plasma amino acids if the diagnosis is considered [86].

Uncertain diagnosis — When there is no metabolic or molecular diagnosis, the empiric recurrence risk for severe microcephaly is high; autosomal recessive inheritance is assumed in many cases.

Autosomal dominant microcephaly is usually milder in all respects and should only be diagnosed if there is a compatible family history (ie, equal frequency in males and females, parent-child transmission, multiple affected generations).

The most common type of autosomal dominant microcephaly is microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (MCLMR, MIM #152950) due to mutations in KIF11 (kinesin family member 11).

In KIF11-dominant primary microcephaly, OFC is -4 to -8 SDs in childhood, but may be normal in adults. Intellectual disability occurs in three-quarters of cases and is usually mild; peripheral lymphedema occurs in one-half and is sometimes problematic [87,88]. Two ophthalmic findings occur in three-quarters of cases: Retinal "lacunae," which appear dramatic but are usually asymptomatic; and familial exudative vitreoretinopathy, which if present needs ophthalmic attention. Almost 10 percent of patients with familial exudative vitreoretinopathy have KIF11 mutations.

In dominant primary microcephaly, a parent is usually affected, and there is dominant family history. However, the OFC can normalize in adult life, so a parental OFC alone does not rule out the diagnosis. Family knowledge (eg, through grandparents) can be invaluable in considering this form of primary microcephaly with good prognosis.

X-chromosome linked forms of microcephaly do exist and this inheritance mechanism must be considered in the case of the solitary affected male.

Clinical genetic follow-up is appropriate when there is no final diagnosis and clinical genetic dilemmas persist. As an example, determining the recurrence risk that is most appropriate for young parents whose first child has severe microcephaly (frequently autosomal recessive, 25 percent recurrence risk) and early onset epileptic encephalopathy (frequently due to de novo, autosomal dominant mutations, less than 5 percent recurrence risk). Detailed DNA sequencing studies (eg, whole genome or whole exome sequencing) may help resolve this type of dilemma. (See 'Second- or "next-generation" sequencing' below.)

GENETIC TESTING

Traditional cytogenetic studies — Cytogenetic studies that have been used to detect chromosome disorders at successively higher resolutions include conventional G-banded chromosome studies and chromosome breakage studies (for DNA repair disorders), fluorescence in situ hybridization studies, supplemented by multiplex ligation-dependent probe amplification studies [89,90]. However, these tests have in total a diagnostic yield of approximately 10 percent in individuals with neurodevelopmental impairments [89]. Although the very rare cytogenetic finding of an increased number of cells in premature prophase occurs in MCPH1 and MSI1 primary microcephalies, these conditions are more easily diagnosed with gene sequencing, so traditional cytogenetic studies are not warranted.

Array comparative genomic hybridization — Array comparative genomic hybridization (array CGH or a microarray) is the cost-efficient, first choice test to seek the large and small genome imbalances that are pathogenic in 10 to 20 percent of cases depending on phenotype selection, with the highest diagnostic yield in children with congenital malformation and dysmorphism [91,92]. The array results should be reviewed promptly (ie, within weeks) to avoid delay in next generation sequencing.

The microdeletions and microduplications that are beyond the resolution of conventional microscopy but which are detected by array CGH are collectively known as copy number variants (CNVs). Some CNVs have well-defined microcephaly phenotypes, whereas others are only tenuously associated or are thought to confer "genetic susceptibility" to a broad range of neurodevelopmental disorders including cognitive impairments, autism, and schizophrenia [93,94]. In families, it often transpires that a CNV, initially thought to be pathogenic, turns out to be inherited from an unaffected parent or a parent who is unaware that they are mildly affected by a developmental disorder or learning disability. All CNV phenotypes are variable to some degree, further complicating assessment. Thus, inheritance studies often are required for the interpretation of abnormal results, and clinical interpretation of array CGH results requires genetics expertise including familiarity with international, collaborative databases of chromosomal variants and their known/potential phenotypes [95]. (See "Microdeletion syndromes (chromosomes 1 to 11)" and "Microdeletion syndromes (chromosomes 12 to 22)" and "Microduplication syndromes".)

Some chromosome microdeletion and microduplication syndromes that are diagnosed through array CGH and can feature microcephaly (typically between two and three standard deviations [SDs] below the mean) are listed in the table (table 3) [96-103].

Molecular genetic testing

First-generation sequencing — First-generation methodology (ie, Sanger sequencing) has been the method of choice for molecular genetic testing in accredited laboratories that analyze patients' DNA seeking single gene mutations that cause neurodevelopmental disorders.

Second- or "next-generation" sequencing — Next-generation ("Next Gen") sequencing, also known as massively parallel sequencing, permits the examination of many genes simultaneously. The application of this new technology, along with huge reductions in cost, presage a new era in molecular genetic testing where it is possible to sequence the entire human genome (whole genome sequencing [WGS]), only the DNA sequences that are transcribed into RNA and translated into protein (exome sequencing), or subsets of specific disease-relevant protein-coding genes (gene panels). A present-day challenge for clinicians who receive next-generation sequencing results is to foster an essential working relationship with the scientists and bioinformaticians, who analyze/filter the many DNA sequence variants each individual carries. Despite the technologic advances, the clinician's skills remain essential to the whole process. The clinician must interpret the family tree and analyze the phenotype, keeping in mind potential pitfalls such as genetic heterogeneity, variable expression of mutant genes, and novel patterns of inheritance. (See "Next-generation DNA sequencing (NGS): Principles and clinical applications".)

The initial successes of next-generation sequencing involved identification of genes for distinctive and exceptionally rare syndromes that there were only ever going to have one or two candidate genes. However, in 2012, independent researchers in Holland, Germany, and the United States demonstrated that "Next Gen," is powerful enough to be used in common clinical settings to identify mutations in genes that cause severe but nonspecific developmental disorders, such as microcephaly, that have many candidate genes [104,105].

Approach to molecular or DNA testing for microcephaly — Molecular genetic testing may be indicated in patients with microcephaly in whom the diagnosis remains uncertain after array CGH or may be performed initially if there is likely to be an excessive wait for the result of array CGH.

In children and adults with occipitofrontal circumference (OFC) more than four SDs below the mean for age, sex, and gestational age and classic primary microcephaly (MCPH) phenotype (ie, reduced OFC from birth, relatively typical brain anatomy, relative absence of neurologic signs, and nonprogressive moderate to severe learning difficulties), first-generation or Sanger sequencing analysis of MCPH5 (ie, seeking mutations in ASPM) may still be warranted, but some laboratories primarily sequence the relevant gene using WGS.

If first-generation sequencing fails to identify a disease-causing variant, the increasing number of microcephaly genes with overlapping phenotypes makes it difficult to formulate a plan for subsequent testing of single genes. Practical considerations, including cost, tend to limit evaluation to one or two microcephaly genes, usually ASPM (for MCPH5) and WDR62 (for MCPH2), which may be analyzed by WGS anyway. Mutations in ASPM are more common [45].

For the inexperienced practitioner, pitfalls of choosing the most appropriate one or two microcephaly gene tests abound. For example, MCPH4 (MIM #604321), a rare variety of primary microcephaly identified in families from North Africa, was initially thought to be due to mutation in the CEP152 gene on chromosome 15q21 [106]. However, a mutation in the cancer susceptibility candidate 5 (CASC5) gene (MIM *609173) on chromosome 15q14 was subsequently identified in the original family with MCPH4 [107,108]. A family with biallelic mutations in both MCPH1 and TRAPPC9 suggests that loss of the c-terminal BRCT3 domain may not cause MCPH [109]. Microcephaly caused by mutation in the CEP152 gene is now designated MCPH9 (MIM #614852), sometimes described as "mild" Seckel syndrome. (Refer to MIM 210600 for a discussion of the genetic heterogeneity in Seckel syndrome.)

Analysis of additional MCPH genes is more cost efficient if it is performed by next-generation DNA sequencing of a "microcephaly gene panel." One such panel analyzed 15 microcephaly genes [110]. Inclusion of KIF11 in the MCPH panel may be warranted; in KIF11-dominant primary microcephaly, the affected parent may have an OFC in the normal range. (See 'Primary genetic microcephaly and its syndromes' above and 'Second- or "next-generation" sequencing' above.)

We suggest taking parental samples and extracting DNA at the first point of contact because comparison of the results of the child's sequence with those of both parents is usually necessary. Careful consideration of the information supplied is necessary to obtain informed consent for any further analysis.

If the array and panel testing are unremarkable, we suggest review of the history and examination. In the absence of additional information that would prompt targeted genetic analysis, we reconsider any metabolic disorders that may explain the presentation and are amenable to treatment. Referral to metabolic services, review of previous results, and obtaining a gene panel for inherited metabolic disorders may be warranted.

Agnostic interrogation of the child's genome in comparison to that of both parents (trio WGS) can be the next stage in genomic analysis or supersede gene panel analysis for both microcephaly and inborn errors of metabolism.

SOCIETY GUIDELINE LINKS — Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: Microcephaly".)

SUMMARY

●Terminology – The definition of microcephaly is not standardized. Microcephaly is variably defined as an occipitofrontal circumference (OFC) of more than two or three standard deviations (SDs) below the mean for a given age, sex, and gestation. Microcephaly is more likely to be associated with disorders affecting brain development if it is defined as more than three SDs below the appropriate mean. (See 'Definition' above.)

●Initial genetics consultation – Isolated microcephaly may be caused by a genetic abnormality or due to acquired pathology (eg, viral infection), and the differentiation is critical. The objective of a genetics consultation for a family with a child or relative affected by microcephaly is to formulate a diagnosis, the more precise the better, and estimate the chance of recurrence of the condition in another child. (See 'Initial genetics consultation' above.)

Chromosome studies are important in all cases where acquired etiology is unlikely, but the method of evaluation is best determined on a case-by-case basis. An array comparative genomic hybridization (array CGH) study (a microarray) is generally the first-line genetic test, particularly when there is less severe microcephaly with dysmorphism. (See 'Laboratory evaluation' above and 'Array comparative genomic hybridization' above.)

●Subsequent genetics assessment

•Primary microcephaly and its syndromes – In children and adults with OFC more than four SDs below the mean for age, sex, and gestational age and classic primary microcephaly (MCPH) phenotype (ie, reduced OFC from birth, relatively typical brain anatomy, relative absence of neurologic signs, and nonprogressive moderate to severe learning difficulties (picture 1)), first-generation genetic analysis for MCPH5 (ie, sequencing for mutations in ASPM) is most likely to detect mutations. Analyses of additional MCPH genes is most cost efficient if performed by next-generation DNA sequencing with a "microcephaly gene panel" (if available). (See 'Primary genetic microcephaly and its syndromes' above and 'Approach to molecular or DNA testing for microcephaly' above.)

•Microcephaly with dysmorphism – In children and adults with OFC between two and three SDs below the mean and static neurologic impairments, learning disability, and dysmorphism, primary microcephaly is unlikely. Chromosome testing by array CGH is the first-line test. Subsequent clinical evaluation is led by the dysmorphologist. (See 'Microcephaly with dysmorphism' above and 'Array comparative genomic hybridization' above.)

•Microcephaly and neurologic abnormalities – The evaluation for children with microcephaly and neurologic abnormalities generally progresses through a series of genetic, radiologic, and biochemical tests, usually led by the neurologist and/or metabolic medicine specialist. (See 'Microcephaly with prominent neurologic abnormalities' above and 'Neuroimaging' above.)

Agnostic interrogation of the child's genome in comparison to that of both parents (trio whole genome sequencing) can be the next stage in genomic analysis or supersede gene panel analysis for both microcephaly and inborn errors of metabolism. (See 'Approach to molecular or DNA testing for microcephaly' above.)

•Uncertain diagnosis – When there is no identified acquired etiology or molecular diagnosis, the empiric recurrence risk for severe microcephaly is high; autosomal recessive inheritance is assumed in many cases. Clinical genetic follow-up is appropriate when there is no final diagnosis and clinical genetic dilemmas persist. (See 'Uncertain diagnosis' above.)

ACKNOWLEDGMENT — The UpToDate editorial staff acknowledges John Tolmie, MB, ChB, FRCP and Geoff Woods, ChB, MB, MD, FRCP, FMedSci, who contributed to earlier versions of this topic review.