Prader-Willi Syndrome Genetics

PWS is a complex genetic syndrome resulting from the absence of expression of imprinted genes found in the region of the paternally inherited 15q11-q13 chromosome; most commonly due to a paternal 15q11-q13 deletion. Three molecular classes are recognized:

  • A paternal de novo deletion of 15q11-q13 (60% of cases);
  • Maternal disomy 15, where both chromosomes 15 come from the mother (35% of cases); and,
  • A small percentage with imprinting defects with a microdeletion of the imprinting center or an epimutation controlling the expression of imprinted genes in the chromosome 15q11-q13 region.

Nearly a dozen genes or transcripts mapped to the 15q11-q13 region are known to be imprinted; most are paternally expressed (active) or maternally silent. Several of these genes are candidates for causing features seen in PWS, including SNURF/SNRPN, NDN, SNORDs, MKRN3, and MAGEL2 . Many of the paternally-expressed genes in the region play a role in brain development and function, key for producing the clinical phenotype seen in PWS.

Most cases of PWS are sporadic; however, at least 30 families have been reported with more than one affected member, including reports in twins. The chance for familial recurrence is estimated to be less than 1%. However, this risk may be as high as 50% in some families where an imprinting defect (resulting from a micro-deletion or epimutation) causes defective control of differentially expressed genes in both the PWS child and the unaffected father. [Butler: 2019]

  • Imprinting is the process by which maternally and paternally derived chromosomes are uniquely chemically modified leading to different expression of a certain gene or genes on those chromosomes depending on their parental origin.
  • An epimutation is a heritable change in the gene expression, such as through DNA methylation, which occurs without changing the base pair sequence of the DNA.

To confirm clinical findings of PWS, genetic testing is recommended. Genetic testing is complex and specialists vary in the approaches they recommend for children suspected of having PWS; consulting a clinical geneticist in your area is advised. If the diagnosis is confirmed, identification of the PWS molecular class is important to guide clinical management and advice regarding recurrence risks.

Advances in genetic technology allow for more accurate and early identification of PWS and genetic subtypes. This includes the larger typical type I deletion involving the proximal 15q11-q13 breakpoint BP1 and the distal 15q11-q13 breakpoint BP3, while the smaller typical type II deletion involves the proximal breakpoint BP2 and the distal breakpoint BP3. Those with the larger type I deletion generally have more behavioral problems. More clinical variation is seen in those with maternal disomy 15 (complete heterodisomy, segmental isodisomy, or total isodisomy of chromosome 15) or in those rare PWS individuals with imprinting defects (microdeletions or epimutations). High recurrence risks (50%) are seen in fathers carrying microdeletions of the imprinting center

To confirm clinical findings of PWS, some clinicians begin with methylation analysis of DNA from the PWS critical region on chromosome 15q11-q13 (99% sensitive).

  • If this test is positive, cytogenetic analysis with FISH (fluorescent in situ hybridization using the SNRPN probes) will identify the 15q11-q13 deletion seen in the majority of subjects (70-75%) but will not determine the size of the deletion. More recently, high-resolution SNP chromosomal microarrays are used, with over 2.5 million probes to detect and identify the typical 15q11-q13 Type I or Type II deletions, atypical deletions (larger and smaller than the typical), maternal disomy 15 subclasses (heterodisomy, segmental isodisomy, total isodisomy), and microdeletion of the imprinting center. FISH is no longer commonly ordered because the specific genetic lesion better determines clinical management, prognosis, and recurrence risks. See Genetic Laboratory Flow Chart for Testing PWS [Hartin: 2019].
  • If the methylation test is negative, PWS is unlikely to be the diagnosis and other diagnoses should be considered. If PWS is still strongly suspected, a clinical genetics evaluation is recommended, which might include next generation sequencing analysis to rule out other disorders that may resemble PWS.
DNA methylation is 99% sensitive but does not differentiate among the potential causes, including small deletions, maternal disomy 15, or an imprinting defect.

MS-MLPA (methylation-specific-multiplex ligation-dependent probe amplification) for DNA analysis of PWS is helpful and undertaken in both clinically approved and research-based laboratories. This DNA kit will determine the DNA methylation pattern using several probes consistent with PWS and will identify the copy number (deletion) for the 15q11-q13 region. However, It will not identify maternal disomy 15 or, necessarily, an imprinting defect. Additional PWS genetic subtypes (maternal disomy 15 and/or imprinting defects) will require CNV/SNP DNA microarray analysis (as described above) or, in a small subset of PWS cases, parental DNA may be required to genotype DNA markers for determining maternal disomy 15 and/or an imprinting defect.

Historically, clinicians preferred to start with a cytogenetic analysis using FISH and SNRPN probes to identify the typical 15q11-q13 deletion. If neither a deletion of chromosome 15 or any other cytogenetic abnormality is identified, DNA methylation testing is then performed. If the methylation study is positive for PWS, then testing for the molecular classes (paternal deletion, maternal disomy or imprinting defect) should be pursued with a SNP microarray test which will identify the genetic cause and molecular class in PWS in about 85% of cases. [Hartin: 2019]

Recent reports of growth hormone (GH) receptor gene polymorphisms that impact growth rate acceleration may guide the monitoring of growth rate in those with PWS particularly while on GH treatment. Testing for a specific polymorphism, which is seen in about 50% of Caucasian individuals and may contribute to the rate of growth and possibly scoliosis, should be considered in the care of PWS infants, children, and adolescents while undertaking GH treatment. [Butler: 2013]

Chromosomal microarrays with polymorphic SNP probes are now used to detect uni-parental disomy (UPD)15 (heterodisomy, segmental isodisomy, total isodisomy) based on loss of heterozygosity (LOH) on chromosome 15. Genotyping of microsatellite markers from chromosome 15 using PCR on both the PWS subject’s and parental DNA will identify biparental (normal) inheritance and imprinting defects in those with abnormal methylation, but with no recognized deletion, or areas of LOH on chromosome 15.

  1. Typical and atypical chromosome 15q11-q13 deletions in PWS are found using high-resolution SNP microarrays, usually 5-6 Mb in size. Regions of homozygosity (ROH) or loss of polymorphic DNA signals can also be determined with this method and seen on a single chromosome. If this ROH is greater than or equal to 8 Mb in size, it is called an LOH and is diagnostic for maternal disomy 15 (UPD15) in PWS when found on chromosome 15.
  2. Maternal disomy 15 (UPD15) is grouped into three separate subclasses depending on the size, number, and location of LOHs (heterodisomy, segmental isodisomy, and total isodisomy) identified by high-resolution SNP microarrays. Total isodisomy results from an LOH of the entire chromosome 15 due to a meiosis II error; segmental isodisomy 15 results from crossover events in chromosome segments during maternal meiosis I; and heterodisomy 15 results when no crossover events occur between the chromosome 15 homologues with non-disjunction of the chromosome 15s. The SNP microarray pattern for maternal heterodisomy 15 appears the same as that seen in normal (control) individuals with no LOHs identified.
  3. The presence of UPD15 and subclasses may impact diagnosis and surveillance for a second genetic condition in addition to PWS, particularly if the mother is a carrier of a gene allele for a recessive disorder. If the disturbed gene is found in the LOH region in either the segmental or total isodisomy 15 form, then the PWS child receives two copies of the same recessive gene for a recessive genetic disorder along with PWS. Hundreds of potentially disease-causing genes are found on chromosome 15. However, those with UPD15 due to maternal heterodisomy without crossover events would not be at increased risk. The UPD15 subclass, therefore, may dictate medical management and preventive care, contributing to the rationale for characterizing PWS molecular classes. [Butler: 2016] [Hartin: 2019] [Hartin: 2018]


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Helpful Articles

Burnside RD, Pasion R, Mikhail FM, Carroll AJ, Robin NH, Youngs EL, Gadi IK, Keitges E, Jaswaney VL, Papenhausen PR, Potluri VR, Risheg H, Rush B, Smith JL, Schwartz S, Tepperberg JH, Butler MG.
Microdeletion/microduplication of proximal 15q11.2 between BP1 and BP2: a susceptibility region for neurological dysfunction including developmental and language delay.
Hum Genet. 2011;130(4):517-28. PubMed abstract / Full Text

Authors & Reviewers

Initial publication: September 2008; last update/revision: September 2019
Current Authors and Reviewers:
Author: Merlin G. Butler, MD, PhD
Funding: This page was developed in partnership with the Heartland Genetic Services Network and was funded in part by a Health Resources Services Administration (HRSA) cooperative agreement (U22MC03962). We appreciate the Prader-Willi Syndrome Association (USA) for their outstanding support of individuals with PWS and their families and for the information they provide on their website – – to which we have provided several links within the Diagnosis Module.
Authoring history
2014: update: Merlin G. Butler, MD, PhDR
2008: update: Alan F. Rope, MDR
2008: first version: Merlin G. Butler, MD, PhDA; Judy L. Welch, RN, BSNA
AAuthor; CAContributing Author; SASenior Author; RReviewer

Page Bibliography

Burnside RD, Pasion R, Mikhail FM, Carroll AJ, Robin NH, Youngs EL, Gadi IK, Keitges E, Jaswaney VL, Papenhausen PR, Potluri VR, Risheg H, Rush B, Smith JL, Schwartz S, Tepperberg JH, Butler MG.
Microdeletion/microduplication of proximal 15q11.2 between BP1 and BP2: a susceptibility region for neurological dysfunction including developmental and language delay.
Hum Genet. 2011;130(4):517-28. PubMed abstract / Full Text

Butler MG, Manzardo AM, Forster JL.
Prader-Willi Syndrome: Clinical Genetics and Diagnostic Aspects with Treatment Approaches.
Curr Pediatr Rev. 2016;12(2):136-66. PubMed abstract
Description of clinical findings and genetic causes in Prader-Willi syndrome with diagnostic aspects, genetic testing, and treatment approaches.

Butler MG, Miller JL, Forster JL.
Prader-Willi Syndrome - Clinical Genetics, Diagnosis and Treatment Approaches: An Update.
Curr Pediatr Rev. 2019;15(4):207-244. PubMed abstract / Full Text

Butler MG, Roberts J, Hayes J, Tan X, Manzardo AM.
Growth hormone receptor (GHR) gene polymorphism and Prader-Willi syndrome.
Am J Med Genet A. 2013;161A(7):1647-53. PubMed abstract / Full Text

Hartin SN, Hossain WA, Francis D, Godler DE, Barkataki S, Butler MG.
Analysis of the Prader-Willi syndrome imprinting center using droplet digital PCR and next-generation whole-exome sequencing.
Mol Genet Genomic Med. 2019;7(4):e00575. PubMed abstract / Full Text

Hartin SN, Hossain WA, Weisensel N, Butler MG.
Three siblings with Prader-Willi syndrome caused by imprinting center microdeletions and review.
Am J Med Genet A. 2018;176(4):886-895. PubMed abstract