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Schaaf-Yang Syndrome via the MAGEL2 Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
MAGEL2 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
15179MAGEL281479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

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

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

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

Schaaf-Yang Syndrome is a neurodevelopmental disorder with significant phenotypic overlap to Prader-Willi syndrome (PWS), which is characterized by severe hypotonia, feeding difficulties, failure to thrive, developmental delay, hypogonadotropic hypogonadism, intellectual disability, behavioral anomalies, strabismus, scoliosis, sleep disturbances, and characteristic facial anomalies (Fountain and Schaaf. 2016. PubMed ID: 28933382).

Schaaf-Yang syndrome is differentiated from PWS based on the presence of joint contractures and lack of hyperphagia, which usually results in morbid obesity (Fountain and Schaaf. 2016. PubMed ID: 28933382; Cassidy et al. 2012. PubMed ID: 22237428). An autism spectrum disorder (ASD) diagnosis is also more frequently reported in individuals with Schaff-Yang Syndrome (75% of affected individuals) compared to those diagnosed with PWS (approximately 25% of individuals) (Fountain and Schaaf. 2016. PubMed ID: 28933382).

ASD encompasses several neurodevelopmental disorders characterized by varying degrees of social impairment, communication ability, and propensity for restricted interests and repetitive behavior(s) (Levy et al. 2009. PubMed ID: 19819542). ASD usually presents by age 3. Diagnosis is based on the degree and severity of symptoms and behaviors (Diagnostic and Statistical Manual of Mental Disorders (DSM-5); McPartland et al. 2016). Comorbidities occur in more than 70% of cases and include intellectual disability (ID), epilepsy, language deficits, and gastrointestinal problems (Sztainberg and Zoghbi. 2016. PubMed ID: 27786181). Recent studies using whole exome trios have identified novel gene candidates, with familial and de novo variants from several hundred genes now implicated in the development of ASD (Bourgeron. 2016. PubMed ID: 27289453).


MAGEL2 (Melanoma antigen-like 2) encodes an ubiquitin ligase enhancer that is necessary for endosomal protein recycling and is highly expressed in the hypothalamus and central nervous system (Schaaf et al. 2013. PubMed ID: 24076603; Doyle et al. 2010. PubMed ID: 20864041; Tacer and Potts. 2017. PubMed ID: 28626083). Paternally-inherited protein truncating variants in MAGEL2 (nonsense and frameshift) have exclusively been reported in individuals with autosomal dominant Schaaf-Yang syndrome as the maternal allele is imprinted (Fountain et al. 2017. PubMed ID: 27195816; Mejlachowicz et al. 2015. PubMed ID: 26365340; Schaaf et al. 2013. PubMed ID: 24076603). Prader-Willi syndrome is generally associated with genomic alterations at the 15q11-13 locus on the paternal allele which encompasses the PWS critical region (MKRN3, MAGEL2, NDN, NAPAP1, SNURF-SNRPN, and small nucleolar RNA genes) (Cassidy et al. 2012. PubMed ID: 22237428; Fountain and Schaaf. 2016. PubMed ID: 28933382; Buiting. 2010. PubMed ID: 20803659).

Individuals with paternally-inherited MAGEL2 full gene deletions have milder phenotypes than those who inherit MAGEL2 protein truncating variants. Individuals with deletions encompassing MAGEL2 but not the SNORD116 locus are generally asymptomatic (with the exception of delayed motor development) and have not been reported to present with joint contractures, ASD, or hyperphagia (Buiting et al. 2014. PubMed ID: 24661356; Kanber et al. 2009. PubMed ID: 19066619). Mouse studies suggest that deletion of the MAGEL2 promoter and coding region may result in partial reactivation of the maternal allele (Matarazzo and Muscatelli. 2013. PubMed ID: 25003016) and thus a milder phenotype. It has also been hypothesized that truncated MAGEL2 has neomorphic activity (Fountain and Schaaf. 2016. PubMed ID: 28933382).

Clinical Sensitivity - Sequencing with CNV PG-Select

Prevalence of Prader Willi syndrome is estimated to range between 1/10,000 to 1/30,000 births and is the most common cause of syndromic obesity in the context of intellectual disability (Angulo et al. 2015. PubMed ID: 26062517). However, approximately 30 individuals with paternally-inherited protein truncating variants in MAGEL2 have been reported in the literature with Schaaf-Yang syndrome (Fountain et al. 2017. PubMed ID: 27195816). Due to paralogy issues from c.1 to c.1845, this tests analytical sensitivity to detect protein truncating variants is less than 100%.

With respect to ASD phenotypes, genetic evaluation of autism spectrum disorder (ASD) patients is estimated to identify a cause in up to 40% of cases. The combined diagnostic yield of chromosomal microarray testing and FMR1 CGG-repeat expansion testing is approximately 11%-15% (Schaefer and Mendelsohn. 2013. PubMed ID: 23519317). The role of nucleotide substitutions and small insertions/deletions in autism-related genes is less clear, but may be as high at 15%, depending on the penetrance of the candidates (Schaefer and Mendelsohn. 2013. PubMed ID: 23519317; Casanova et al. 2016. PubMed ID: 26985359). To date, almost 1,000 genes have documented associations with ASD. It has been reported that nearly 60% of the total variation occurs in approximately 200 genes each of which have several ASD-associated variants (Stenson et al. 2014. PubMed ID: 24077912).

Testing Strategy

This test is performed using Next-Generation sequencing with additional Sanger sequencing as necessary.

This test provides partial coverage of the single coding exon of the MAGEL2 gene. We define full coverage as >20X NGS reads or Sanger sequencing.

Due to sequence paralogy issues, we are unable to Sanger confirm variants called by NGS within MAGEL2 (NM_019066.4) from c.1 to c.1845 (g.23891045).

Indications for Test

De novo and paternally-inherited MAGEL2 variants (due to imprinting of the maternal allele at this locus) have been reported to date. A panel (or exome/genome) sequencing test would nearly always be more appropriate for patients with ASD, unless previous clinical knowledge or features implicates the MAGEL2 gene. For example, an affected individual with a paternal family member having a known MAGEL2 variant and similar clinical features to PWS or Schaaf-Yang syndrome may consider MAGEL2 testing (targeted Sanger sequencing for the known variant may be most appropriate).


Official Gene Symbol OMIM ID
MAGEL2 605283
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Schaaf-Yang Syndrome AD 615547


  • Angulo et al. 2015. PubMed ID: 26062517
  • Bourgeron. 2016. PubMed ID: 27289453
  • Buiting et al. 2014. PubMed ID: 24661356
  • Buiting. 2010. PubMed ID: 20803659
  • Casanova et al. 2016. PubMed ID: 26985359
  • Cassidy SB, Schwartz S, Miller JL, Driscoll DJ. 2012. Prader-Willi syndrome. Genet Med 14: 1026 PubMed ID: 22237428
  • Doyle et al. 2010. PubMed ID: 20864041
  • Fountain and Schaaf. 2016. PubMed ID: 28933382
  • Fountain et al. 2017. PubMed ID: 27195816
  • Kanber et al. 2009. PubMed ID: 19066619
  • Levy et al. 2009. PubMed ID: 19819542
  • Matarazzo and Muscatelli. 2013. PubMed ID: 25003016
  • McPartland J.C. et al. 2016. Encyclopedia of Mental Health. 2: 124-130
  • Mejlachowicz et al. 2015. PubMed ID: 26365340
  • Schaaf et al. 2013. PubMed ID: 24076603
  • Schaefer and Mendelsohn. 2013. PubMed ID: 23519317
  • Stenson et al. 2014. PubMed ID: 24077912
  • Sztainberg and Zoghbi. 2016. PubMed ID: 27786181
  • Tacer and Potts. 2017. PubMed ID: 28626083


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

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