1. NGS panel - Genetic testing for Microcephaly


July 19, 2017

Disease synonyms

Microcephaly, MCPH, Seckel syndrome, SCKL

Inheritance pattern

Autosomal recessive, X-linked, autosomal dominant

Clinical features

Seckel syndrome is rare autosomal recessive disorder characterized by intrauterine growth retardation, dwarfism, microcephaly with mental retardation, and a characteristic 'bird-headed' facial appearance. The major feature of Seckel syndrome is associated autosomal recessive primary microcephaly (MCPH). Microcephaly is a neurodevelopmental condition characterized by microcephaly present at birth, decreased cerebral cortex size, and non-progressive mental retardation with the absence of visceral abnormalities.

Primary microcephaly has an incidence of less than 1 (0.68) 10,000 in Australia 1, 1:30,000 in Japan 2, 1:250,000 in Netherlands 2 and 1:2,000,000 in Scotland 2, 3.

Microcephaly is divided into primary microcephaly, which is present at birth, and secondary microcephaly, which develops postnatally 4. The crucial difference between these groupings is that primary microcephaly is usually a static developmental anomaly, whereas secondary microcephaly indicates a progressive neurodegenerative condition 5.

Microcephaly Infographics

The major clinical features of microcephaly include the following:

  • Prenatal onset, during the second trimester of gestation
  • Reduced occipito-frontal circumference (OFC) at birth (<-2 SD) 3. Microcephaly tends to worsen over time and after 6 months of age OFC is at least -3 SD, while it ranges between -4 and -12 SD (mean -8 SD) in older individuals 3.
  • Reduced volume of the cerebral hemispheres, commonly reduced to one third of normal, while the organization and topography of gyri are normal but the pattern may be simplified
  • Reduced size of hindbrain and cerebellum
  • A significant correlation between the severity of microcephaly and both the degree of simplified gyration and the reduction of white matter volume
  • In cases with more severe microcephaly corpus callosum is thinner 6
  • In some affected individuals neuronal migration is abnormal, resulting in heterotopias, or focal pachygyria or polymicrogyria 7.

Cognitive impairment is present in a majority of persons with microcephaly and it ranges from mild to moderate without major motor delay. More severe cognitive impairment has been observed in individuals with Seckel syndrome and in those with isolated microcephaly with brain malformations 3.

A common finding in microcephaly is also short stature, typically between -1 SD and -2 SD and in Seckel syndrome it ranges between -4 and -12 SD 3. Some affected individuals may develop craniosynostosis, secondary to insufficient and slow head growth.

There are many nongenetic and genetic causes of primary microcephaly, such as maternal alcohol overconsumption during pregnancy, congenital infection with toxoplasma, and Rubenstein Taybi syndrome. Microcephaly can be associated with hundreds of syndromal congenital anomalies, including many chromosomal disorders. Microcephaly is also a frequent sign of defects in DNA repair mechanisms and in nucleotide excision repair, in which it often is associated with general growth impairment.

There are a number of genes which have been associated with microcephaly, including the following genes (see Table):

  • Microcephaly phenotype only: MCPH1 (MCPH1), WDR62 (MCPH2), CDK5RAP2 (MCPH3), KNL1 (MCPH4), ASPM (MCPH5), STIL (MCPH7), CEP135 (MCPH8), and CDK6 (MCPH12)
  • Seckel syndrome phenotype only: ATR (SCKL1), NIN (SCKL7), and ATRIP
  • Microcephaly with Seckel syndrome and/or intermediate phenotypes: RBBP8 (SCKL2), CEP152 (MCPH9/SCKL5), CENPJ (MCPH6/SCKL4), CEP63 (SCKL6), and PHC1 (MCPH11).

Table 1. Overview of genes associated with Microcephaly

Gene OMIM (Gene) Associated diseases (OMIM) Inheritance CentoMD® exclusive variant numbers (++)
AKT3 611223 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 AD 3
AP4M1 602296 Spastic paraplegia 50, autosomal recessive AR 13
ARFGEF2 605371 Periventricular heterotopia with microcephaly AR 13
ASPM 605481 Microcephaly 5, primary, autosomal recessive AR 21
ASXL3 615115 Bainbridge-Ropers syndrome AD 6
ATR 601215 Seckel syndrome 1; ?Cutaneous telangiectasia and cancer syndrome, familial AD, AR 17
ATRX 300032 Alpha-thalassemia myelodysplasia syndrome, somatic; Alpha-thalassemia/mental retardation syndrome; Mental retardation-hypotonic facies syndrome, X-linked XL D, XL R 11
CASK 300172 FG syndrome 4; Mental retardation, with or without nystagmus; Mental retardation and microcephaly with pontine and cerebellar hypoplasia XL D 17
CDK5RAP2 608201 Microcephaly 3, primary, autosomal recessive AR 11
CDK6 603368 ?Microcephaly 12, primary, autosomal recessive AR 0
CENPE 117143 ?Microcephaly 13, primary, autosomal recessive AR 5
CENPF 600236 Stromme syndrome AR 12
CENPJ 609279 Microcephaly 6, primary, autosomal recessive; ?Seckel syndrome 4 AR 17
CEP135 611423 Microcephaly 8, primary, autosomal recessive AR 16
CEP152 613529 Seckel syndrome 5; Microcephaly 9, primary, autosomal recessive AR 8
CEP63 614724 ?Seckel syndrome 6 AR 22
CHMP1A 164010 Pontocerebellar hypoplasia, type 8 AR 5
CRIPT 604594 Short stature with microcephaly and distinctive facies AR 0
DYRK1A 600855 Mental retardation, autosomal dominant 7 AD 10
EFTUD2 603892 Mandibulofacial dysostosis, Guion-Almeida type AD 25
IER3IP1 609382 Microcephaly, epilepsy, and diabetes syndrome AR 2
KATNB1 602703 Lissencephaly 6, with microcephaly AR 1
KIF11 148760 Microcephaly with or without chorioretinopathy, lymphedema, or mental retardation AD 27
KNL1 609173 Microcephaly 4, primary, autosomal recessive AR 7
MCPH1 607117 Microcephaly 1, primary, autosomal recessive AR 22
MED17 603810 Microcephaly, postnatal progressive, with seizures and brain atrophy AR 1
MFSD2A 614397 Microcephaly 15, primary, autosomal recessive AR 1
MSMO1 607545 Microcephaly, congenital cataract, and psoriasiform dermatitis AR 4
NDE1 609449 ?Microhydranencephaly; Lissencephaly 4 (with microcephaly) AR 2
NHEJ1 611290 Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation 9
NIN 608684 ?Seckel syndrome 7 AR 4
ORC1 601902 Meier-Gorlin syndrome 1 AR 0
PCNT 605925 Microcephalic osteodysplastic primordial dwarfism, type II AR 48
PHC1 602978 ?Microcephaly 11, primary, autosomal recessive AR 4
PLK4 605031 Microcephaly and chorioretinopathy, autosomal recessive, 2 AR 1
PNKP 605610 Microcephaly, seizures, and developmental delay; Ataxia-oculomotor apraxia 4 AR 28
PYCR2 616406 Leukodystrophy, hypomyelinating, 10 AR 1
QARS 603727 Microcephaly, progressive, seizures, and cerebral and cerebellar atrophy AR 2
RBBP8 604124 Jawad syndrome; Seckel syndrome 2 AR 7
SASS6 609321 ?Microcephaly 14, primary, autosomal recessive AR 0
SLC25A19 606521 Microcephaly, Amish type; Thiamine metabolism dysfunction syndrome 4 (progressive polyneuropathy type) AR 6
STAMBP 606247 Microcephaly-capillary malformation syndrome AR 1
STIL 181590 Microcephaly 7, primary, autosomal recessive AR 10
TRMT10A 616013 Microcephaly, short stature, and impaired glucose metabolism 1 AR 0
TUBB2B 612850 Cortical dysplasia, complex, with other brain malformations 7 AD 4
TUBGCP4 609610 Microcephaly and chorioretinopathy, autosomal recessive, 3 AR 0
TUBGCP6 610053 Microcephaly and chorioretinopathy, autosomal recessive, 1 AR 37
WDR62 613583 Microcephaly 2, primary, autosomal recessive, with or without cortical malformations AR 22
ZEB2 605802 Mowat-Wilson syndrome AD 34
ZNF335 610827 ?Microcephaly 10, primary, autosomal recessive AR 2

Abbreviations: MPPH-Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome; SPG-Spastic paraplegia; ARPHM-Autosomal recessive periventricular heterotopia with microcephaly; BRPS-Bainbridge-Ropers syndrome; SCKL-Seckel syndrome; FCTCS-Familial cutaneous telangiectasia and cancer syndrome; MRXHF-Mental retardation-hypotonic facies syndrome; ATRX-Alpha-thalassemia/mental retardation syndrome ATMDS-Alpha-thalassemia myelodysplasia syndrome, somatic; MICPCH-Mental retardation and microcephaly with pontine and cerebellar hypoplasia; FGS-FG syndrome; PCH-Pontocerebellar hypoplasia; MRD-Mental retardation autosomal dominant; MFDGA-Mandibulofacial dysostosis Guion-Almeida type; MEDS-Microcephaly, epilepsy, and diabetes syndrome; LIS-Lissencephaly; MCCPD-Microcephaly, congenital cataract, and psoriasiform dermatitis; MHAC-Microhydranencephaly; SCID-Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation; MCCRP-Microcephaly and chorioretinopathy; MCSZ-Microcephaly, seizures, and developmental delay; AOA-Ataxia-oculomotor apraxia; HLD-Hypomyelinating leukodystrophy; JWDS-Jawad syndrome; THMD-Thiamine metabolism dysfunction syndrome; MICCAP-Microcephaly-capillary malformation syndrome; MSSGM-Microcephaly, short stature, and impaired glucose metabolism; PMGYSA-Polymicrogyria, symmetric or asymmetric; MOWS-Mowat-Wilson syndrome.

Treatment for patients affected with microcephaly commonly includes supportive therapy, including special education, speech and language therapy, behavioral therapy, occupational therapy, and community services for families. Ritalin® may be helpful in managing hyperkinesia 3. Seizures are usually responsive to monotherapy with standard antiepileptic drugs (AEDs).

CENTOGENE offers full gene sequencing and deletion/duplication analysis for the Microcephaly panel (genes: AKT3, AP4M1, ARFGEF2, ASPM, ASXL3, ATR, ATRX, CASC5, CASK, CDK5RAP2, CDK6, CENPE, CENPF, CENPJ, CEP135, CEP152, CEP63, CHMP1A, CRIPT, DYRK1A, EFTUD2, IER3IP1, KATNB1, KIF11, MCPH1, MED17, MFSD2A, MSMO1, NDE1, NHEJ1, NIN, ORC1, PCNT, PHC1, PLK4, PNKP, PYCR2, QARS, RBBP8, SASS6, SLC25A19, STAMBP, STIL, TRMT10A, TUBB2B, TUBGCP4, TUBGCP6, WDR62, ZEB2, ZNF335).

Differential diagnosis

The differential diagnosis of microcephaly-related disorders – depending on the major symptoms in the initial case – includes the following diseases:

  • Anencephaly
  • Down Syndrome
  • Fetal Alcohol Syndrome
  • Pediatric Craniosynostosis
  • Rett Syndrome
  • Spina Bifida

Testing strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for microcephaly using NGS Panel Genomic targeted towards this specific phenotype:

Step 1: Whole genome sequencing from a single filter card. The sequencing covers the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the microcephaly panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the microcephaly panel, we recommend continuing the bioinformatics analysis of the data obtained through whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.

Referral reasons

The following individuals are candidates for microcephaly testing:

  • Individuals with a family history of microcephaly and presentation of the most common symptoms
  • Individuals without a positive family history, but with symptoms resembling microcephaly
  • Individuals with a negative but suspected family history of microcephaly, in order to perform proper genetic counseling.

Test utility

Sequencing, deletion/duplication of the panel genes should be performed in all individuals suspected of having microcephaly and suspected phenotypes. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of the microcephaly and related disorders identify at-risk family members, provide disease risks as well as appropriate referral for patient support and/or resources.

More information on CENTOGENE´s Microcephaly panel can be found in our genetic test catalogue.