Whole exome sequencing identifies a novel homozygous frameshift mutation in the ASPM gene, which causes microcephaly 5, primary, autosomal recessive

Introduction

Microcephaly with no other anomalies in the brain structure is termed as true microcephaly or autosomal recessive primary microcephaly (MCPH), where the pathology of brain is generally congenital and static with mild to moderate intellectual disability (ID) (http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Expert=2512). Microcephaly is seen in numerous syndromes¹ and even in true microcephaly, there is possibility of more than one gene implicated^2,3, thus screening for a single gene may not be very fruitful in this population. Recently, whole exome sequencing (WES) has emerged as a potential approach to delineate the molecular pathology in the microcephaly population with ID¹. Using WES, we report a de novo frame shift (insertion) mutation in the calponin-homology domain of ASPM (Abnormal Spindle-Like, Microcephaly-Associated) gene which is a candidate for MCPH5 (Microcephaly 5, primary, autosomal recessive) in a client with true microcephaly.

Report

The client sequenced was under the research project cerebral palsy and spectrum conditions (seizures, mental retardation, microcephaly and other neurodevelopmental disorders), which aims to find disease causing mutations in a sample of 100 clients recruited from our Motor Speech Disorders Clinic at Department of Clinical Services, All India Institute of Speech and Hearing. This is a research project and hence ethical clearance was obtained, reference was mentioned in Methods. The client is a 15 year old female born out of a consanguineous union (parents were first cousins) diagnosed with microcephaly (occipitofrontal head circumference was 40 centimetres) and developmental delay. The mother had a history of one miscarriage at the third month of gestation and a still birth (female) at the eighth month (Figure 1A). An ultra sound scan of the foetus (client) at the eight month of pregnancy revealed delayed development. The client was born at term through normal delivery with no birth trauma. Her younger brother was clinically normal. The client had a squint at birth and had mild ID. At age 12 years, her developmental age was between 66 to 78 months as assessed by the Developmental Screening Test (DST)⁴. Her Receptive Language Age (RLA) and Expressive Language Age (ELA) was 18–20 months as revealed by Receptive Expressive Emergent Language Scale (REELS)⁵. She had a vocabulary of around 50 words and was able to comprehend commands, would recognize family members and common objects. She expressed herself through single word utterances, gestures and pointing.

Figure 1.

(A) The pedigree of the family; (B) workflow of the variant prioritization.

Results

Discussion

ASPM protein determines cerebral cortical size. During initial stages of corticogenesis, the ASPM protein is essential in facilitating the proliferation of neural progenitors⁶. This process determines the cerebral cortical volume⁷ which has tripled over the last ~ 2 million years, leading to exceptionally big brain in humans compared to their primate counterparts⁸. This increase in the human brain size is believed to be one contributing factor for the emergence of higher cognitive function and language ability that are restricted to humans⁸. So far, 17 genes have been reported in which, mutations lead to the development of MCPH^3,4,9–26. The phenotype(s) arising from pathogenic variants in these 17 genes are each named from MCPH 1 – MCPH 17 (there are 17 genes identified so far that cause autosomal recessive primary microcephaly, MCPH arising from these 17 genes are termed from MCPH 1 to MCPH 17) and the majority of the genetic load in MCPH is contributed by the ASPM gene, making MPCH5 the most prevalent of all the types of MCPH. Frame shift and protein truncating mutations in ASPM cause MCPH5 and these mutations are restricted to be seen in homozygous state only in the MCPH5 population^27,28 (i.e., heterozygous mutations does not have any effect and only homozygous mutations will cause the MCPH).

Conclusion

The novel insertion mutation found in the ASPM gene in the present study segregated with the phenotype in the family, establishes the role of the novel frame shift mutation identifiedin the development of MCPH5 in the case studied. Candidate gene study by Sanger sequencing is time consuming and not economical when compared to WES. Given its higher diagnostic yield as evident by published studies on neurodevelopmental disorders² and also from the present work, we support the findings reported by Rump et al. (2016) which states that WES in microcephaly population will end unnecessary further evaluations and aid in early appropriate interventions².

Consent

Written informed consent to carry out the study and for the publication of the client’s and client’s sibling’s clinical details were obtained from the parents. Clinical details were obtained from the parents of the client.

Data availability

Sequence data for the insertion mutation (client sample) was deposited in Genbank under accession number MG063723.