Angelman Syndrome via the UBE3A Gene

Angelman syndrome (AS) is a neurodevelopmental disorder characterized by severe developmental delay, intellectual disability, speech impairment, seizures and characteristic behavior with an inappropriate happy demeanor with easily provoked laughter, short attention span, smiling and excitability. Individuals with AS plateau at a developmental level of 24 to 30 months, and cognitive performance usually shows severe functional impairment. Most children with AS have reduced need for sleep, and frequent awakening at night is common (Lossie et al. 2001). Fifty percent of the children develop microcephaly (Occipital Frontal Circumference < 2SD) by the age of 12 months. All children with AS have some component of hyperactivity with seemingly ceaseless activity. Language impairment is severe with most individuals lacking speech entirely, but a few develop single-word vocabularies. A large subset of children with AS qualify for a comorbid diagnosis of autism. A subset of AS patients also have hypopigmentation of the skin, hair and eyes, attributable to haploinsufficiency of OCA2 gene (due to maternal deletion) located close to the UBE3A gene. The prevalence of AS is one in 12,000-20,000.

Differential diagnoses with several overlapping features with AS include Mowat-Wilson syndrome (Test #1567), X-linked Christianson syndrome (Test #562 and Test #600), Rett syndrome (Test #1455 and Test #600), Pitt-Hopkins syndrome (Tests #1523, #1522 and #600), 2q23.1 deletion syndrome (Test #1321), and Phelan-McDermid syndrome (Test #600).

The AS and related Prader-Willi syndrome (PWS) region is localized to a 5-6 Mb genomic region on the proximal long arm of chromosome 15 (15q11.2-q13). This region contains several genes that are differentially expressed depending on whether the region is inherited from the father or the mother, i.e., some genes in this regions are expressed only from the paternal chromosome and some expressed only from the maternal chromosome. This differential gene expression is achieved by differential methylation (imprinting) pattern on the paternal and maternal chromosomes. The PWS paternally-only expressed region contains five genes (MKRN3, MAGEL2, NDN, NPAP1, and SNURF-SNRPN), one ORF (C15orf2), and a family of small nucleolar RNA (snoRNA) genes or gene clusters. The AS maternally-only expressed region contains one gene, UBE3A. Deletion mapping in PWS/AS patients identified two small regions of deletion overlap (SRO) that define two critical imprinting centers (IC). PWS-SRO is a 4.3 kb region that lies at the 5’ end of the bicistronic SNURF-SNRPN, and has CpG islands encompassing the promoter, exon 1 and intron 1 of SNURF-SNRPN. AS-SRO is 880bp in size and maps 35 kb proximal to the SNURF-SNRPN exon 1.

AS is caused by loss of a functional UBE3A gene on maternally inherited chromosome 15q11.2-q13. Loss of this maternally expressed gene at 15q11.2-13 can arise from several different genetic mechanisms. Approximately 65-75% of AS patients have a recurrent deletion of 15q11.2-13 on the maternally inherited chromosome, ~3-7% have a paternal uniparental disomy (UPD) of chromosome 15, 3% have imprinting defect (ID) i.e., mutations within the imprinting control region that establish a paternal methylation pattern despite the presence of bi-parental chromosomes (approximately 10-15% of the AS individuals with ID have a very small deletion in the AS IC), and 5-10% of AS patients have mutations in the UBE3A gene (Williams et al. 2010; Dagli et al. 2012).

Alternatively, absence or loss of expression of paternally expressed genes lead to PWS (Test #2056).

Sequence analysis of individuals with AS reveals that the majority of UBE3A mutations result in protein truncation. More than 60 causative mutations have been reported and 60-70% of these include small deletions and duplications leading to frame shift mutations. Approximately 25% include missense and nonsense mutations with the reminder includes splicing defects and gross deletions (Malzac et al. 1998). UBE3A encodes an E3 ubiquitin-protein ligase which is a component of the ubiquitin protein degradation system.

Approximately 10% of AS cases will exhibit causative mutations through sequencing (Sadikovic et al. 2014). Regulatory mutations, deep intronic mutations and large deletions and duplications cannot be detected by this method.

Less than 1% of the AS cases will be diagnosed by this assay.

Methylation analysis of the PWS/AS IC is by far the most efficient starting point for a genetic diagnosis of AS based on a clinical suspicion alone, as it can be used for all three classes of molecular defects (deletion, UPD and Imprinting defect). This method should be the first test ordered on a clinical suspicion of AS (Test #2056). Sequencing of UBE3A should be considered for patients that fit the classic AS phenotype and have normal methylation analysis at the 15q11.2-q13 region. A few individuals with AS have been found to have whole-gene, multi-exonic or intragenic deletions of the UBE3A gene (Boyes et al. 2006, Calì et al. 2010, Sato et al. 2007). A UBE3A deletion/duplication analysis via aCGH (Test #600) should be considered for individuals with a normal methylation pattern and absence of UBE3A truncating mutations.