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Angelman Syndrome by MS-MLPA

Summary and Pricing

Test Method

Methylation-specific Multiplex Ligation-dependent Probe Amplification
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
2056 UBE3A 81331 81331 $540 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
2056UBE3A81331 81331 $540 Order Options and Pricing

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Greg Fischer, PhD

Clinical Features and Genetics

Clinical Features

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 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, X-linked Christianson syndrome, Rett syndrome, Pitt-Hopkins syndrome, 2q23.1 deletion syndrome, and Phelan-McDermid syndrome.


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) patterns on the paternal and maternal chromosomes. The PWS paternally-only expressed region contains five protein coding genes (MKRN3, MAGEL2, NDN, NPAP1, and SNURF-SNRPN), one ORF (C15orf2), and a family of small nucleolar RNA (snoRNA) genes. 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 absence of a functional UBE3A gene on the maternally inherited chromosome. Loss of maternally expressed genes at 15q11.2-13 can arise from several different genetic mechanisms. Approximately 65-75% of the AS patients have a recurrent deletion of the 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 establishes a paternal methylation pattern on the maternal chromosome (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 point mutations in the maternally inherited UBE3A gene (Williams et al. 2010; Dagli et al. 2012).

Around 10% of the patients with a clinical diagnosis of AS have no discernable abnormality at the 15q11.2-q13 region. Some of these patients include mosaic cases of imprinting defects, but a majority result from unidentified defects in UBE3A or mutations in other genes.

Alternatively, absence or loss of expression of paternally expressed genes at 15q11.2-13 lead to PWS.

Clinical Sensitivity - MS-MLPA

Approximately 78% of AS cases will be detected by this assay. Because of simultaneous detection of both copy number and methylation status, MS-MLPA is able to differentiate between AS caused by maternal deletion and those caused by paternal UPD or ID. If no deletion is present, DNA polymorphism analysis will be necessary to differentiate between maternal UPD and ID. This method cannot detect AS caused other molecular mechanisms, including UBE3A point mutations.

Testing Strategy

Methylation analysis (Nygren et al. 2005) 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). Additionally, methylation analysis differentiates between PWS and AS for patients with 15q11.2-q13 deletion without the need for the analysis of parental samples. Methylation analysis makes use of the differentially methylated maternal and paternal chromosome region at 15q11.2-q13 to identify maternal-only, paternal-only or bi-parental inheritance.

At PreventionGenetics we use commercially available methylation-specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA) for the diagnosis of PWS and AS (Procter et al. 2006). This method combines both DNA methylation analysis and copy-number analysis across the entire PWS/AS region. MS-MLPA contains 32 dosage-sensitive probes (for copy number detection) specific for the 15q11.2 region, and five probes determine the DNA methylation status at differentially methylated sites in 15q11.2. Additionally, the dosage-sensitive probes cover SNORD116, one of the snoRNA gene clusters in the PWS/AS region (Ramsden et al. 2010).

The advantages of MS-MLPA method include;

1) Combined detection of both copy-number and methylation status.

2) Can differentiate between PWS caused by paternal deletion or UPD/Imprinting defect.

3) Detection of methylation status at five distinct differentially methylated regions (instead of one locus).

4) Detection of small deletions encompassing IC and SNORD116 gene cluster.

5) Detects more than 78% of the AS cases.

AS patients with normal methylation analysis of the 15q11.2-q13 region should reflex to UBE3A gene sequencing followed if necessary by UBE3A deletion/duplication analysis via aCGH.

Indications for Test

Indications for testing include confirmation of clinical diagnosis of AS and reflex testing after a positive deletion test using CMA or FISH.


Official Gene Symbol OMIM ID
UBE3A 601623
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Angelman Syndrome 105830

Related Tests

2q23.1 Microdeletion Syndrome and Autism Spectrum Disorder via the MBD5 Gene
Angelman Syndrome via the UBE3A Gene
Autosomal-Recessive Intellectual Disability via the NRXN1 Gene
Christianson Type X-Linked Mental Retardation via the SLC9A6 Gene
Mowat-Wilson Syndrome via the ZEB2 Gene
Phelan-Mcdermid Syndrome, 22q13 Deletion Syndrome, or Autism Spectrum Disorder via the SHANK3 Gene
Prader-Willi Syndrome (PWS) by MS-MLPA


  • Dagli A, Buiting K, Williams CA. 2012. Molecular and Clinical Aspects of Angelman Syndrome. Mol Syndromol 2: 100–112. PubMed ID: 22670133
  • Lossie A, Whitney M, Amidon D, Dong H, Chen P, Theriaque D, Hutson A, Nicholls R, Zori R, Williams C, Driscoll D. 2001. Distinct phenotypes distinguish the molecular classes of Angelman syndrome. J Med Genet 38: 834–845. PubMed ID: 11748306
  • Nygren AOH, Ameziane N, Duarte HMB, Vijzelaar RNCP, Waisfisz Q, Hess CJ, Schouten JP, Errami A. 2005. Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences. Nucleic Acids Res 33: e128. PubMed ID: 16106041
  • Procter M, Chou L-S, Tang W, Jama M, Mao R. 2006. Molecular Diagnosis of Prader–Willi and Angelman Syndromes by Methylation-Specific Melting Analysis and Methylation-Specific Multiplex Ligation-Dependent Probe Amplification. Clinical Chemistry 52: 1276–1283. PubMed ID: 16690734
  • Ramsden SC, Clayton-Smith J, Birch R, Buiting K. 2010. Practice guidelines for the molecular analysis of Prader-Willi and Angelman syndromes. BMC Med Genet 11: 70. PubMed ID: 20459762
  • Williams CA, Driscoll DJ, Dagli AI. 2010. Clinical and genetic aspects of Angelman syndrome. Genet Med 12: 385–395. PubMed ID: 20445456


Ordering Options

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myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
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  • Billing information along with specimen and shipping instructions are within the requisition form.
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Specimen Types

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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