Research Article: A Novel Nonsense CDK5RAP2 Mutation in a Somali Child With Primary Microcephaly and Sensorineural Hearing Loss

Date Published: October 10, 2012

Publisher: Wiley Subscription Services, Inc., A Wiley Company

Author(s): Alistair T Pagnamenta, Jennie E Murray, Grace Yoon, Elham Sadighi Akha, Victoria Harrison, Louise S Bicknell, Kaseem Ajilogba, Helen Stewart, Usha Kini, Jenny C Taylor, David A Keays, Andrew P Jackson, Samantha JL Knight.


Primary microcephaly is a genetically heterogeneous condition characterized by reduced head circumference (−3 SDS or more) and mild-to-moderate learning disability. Here, we describe clinical and molecular investigations of a microcephalic child with sensorineural hearing loss. Although consanguinity was unreported initially, detection of 13.7 Mb of copy neutral loss of heterozygosity (cnLOH) on chromosome 9 implicated the CDK5RAP2 gene. Targeted sequencing identified a homozygous E234X mutation, only the third mutation to be described in CDK5RAP2, the first in an individual of non-Pakistani descent. Sensorineural hearing loss is not generally considered to be consistent with autosomal recessive microcephaly and therefore it seems likely that the deafness in this individual is caused by the co-occurrence of a further gene mutation, independent of CDK5RAP2. Nevertheless, further detailed clinical descriptions of rare CDK5RAP2 patients, including hearing assessments will be needed to resolve fully the phenotypic range associated with mutations in this gene. This study also highlights the utility of SNP-array testing to guide disease gene identification where an autosomal recessive condition is plausible. © 2012 Wiley Periodicals, Inc.

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Mutations in ASPM and WDR62 account for the majority of patients with primary microcephaly [Bond et al., 2002; Nicholas et al., 2010]. Five other causative genes are known but have only been reported in a few individuals (for recent review see [Mahmood et al., 2011]). A recent study suggests CEP135 may be responsible for an eighth microcephaly locus on chromosome 4q12 [Hussain et al., 2012]. The fact that the majority of these microcephaly genes were mapped using consanguineous kindreds from Pakistan highlights the importance of the autozygosity mapping strategy in the understanding of this rare condition. However, as a consequence, it is unclear what clinical relevance these genes have in other populations.

The patient was born to Somali parents at 40 weeks gestation, weighing 2.37 kg (−2.39 SDS) with an occipito-frontal head circumference (OFC) of 30cm (−3.68 SDS) and length of 43 cm (−3.68 SDS). Auditory brainstem response testing at 3 days of life was normal. Although there were no neonatal problems, she experienced significant gastro-oesophageal reflux during the first 4 months and was fed via a gastrostomy (aged 9 months). Early developmental milestones were delayed. A brain MRI performed at 15 months showed microcephaly but no structural abnormalities (Fig. 1A). Development was assessed aged 3 using the Vineland Adaptive Behaviour scale: function was between the 1st and 6th percentiles for various domains of development with communication, motor, and composite adaptive behavior skills on the 1st centile and social and daily living skills on the 6th and 5th centiles, respectively. Moderate-to-severe bilateral sensorineural hearing loss was diagnosed at 3 years, 10 months. Molecular testing of GJB2 and GJB6 was normal. Although language skills progressed following the introduction of hearing aids, at 6 years she communicates largely by gestures. She is described as a happy, sociable child with no reported behavioral problems. At 6 years, growth parameters were: weight 17.6 kg (−1.12 SDS), height 107.5 cm (−1.61 SDS), and OFC 41.5 cm (−8.91 SDS), with a sloping forehead (Fig. 1B). There was mild joint laxity, hypotonia, and decreased muscle bulk. No maternal or environmental causes were identified that may have contributed to the microcephaly or deafness. Given the absence of associated malformations or neurological deficits, a clinical diagnosis of primary microcephaly was made. ASPM was sequenced but no mutations were identified.

The genome-wide SNP analysis did not reveal any copy number variants (CNVs) in the patient, other than those noted already in the Database of Genomic Variants. However, two large tracts of cnLOH involving chr7p15.2–p21.3 and chr9q33.1–q34.12 (Fig. 1C) were noted of greater than 5 Mb. These were not observed in the mother. Co-occurrence of two independent cnLOH regions led us to consider an unreported consanguineous parental relationship. The coefficient of inbreeding (fraction of the genome showing cnLOH) was estimated to be ∼1/95, consistent with parents who are second-cousins or second-cousins-once-removed. Subsequent re-evaluation of family-history established that parents were indeed second-cousins (Fig. 1D).

To date, only two disease-causing mutations in CDK5RAP2 have been described, both in consanguineous families; a Y82X mutation [Bond et al., 2005; Hassan et al., 2007] and a IVS26-15A>G splicing mutation [Bond et al., 2005] (Table I). All three published families are from Northern Pakistan. Therefore, our report of a Somali child with primary microcephaly and a novel E234X mutation confirms CDK5RAP2 as a disease gene with clinical relevance outside the Pakistani population.




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