You are here: Home / Rare Disease Information / Rare Disease Database

Search Rare Diseases

Enter a disease name or synonym to search NORD's database of reports.

0-9 - A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z

Pallister Hall Syndrome

NORD is very grateful to Daniel Balcarcel, NORD Editorial Intern from the University of Notre Dame, and Leslie G Biesecker, MD, Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, for assistance in the preparation of this report.

Synonyms of Pallister Hall Syndrome

  • CAVE (cerebro-acro-visceral early lethality) complex
  • congenital hypothalamic hamartoblastoma syndrome
  • Hall-Pallister syndrome
  • PHS

Disorder Subdivisions

  • No subdivisions found.

General Discussion

Pallister-Hall syndrome (PHS) is an extremely rare genetic disorder that is typically apparent at birth. The symptoms and findings associated with the disorder may vary greatly in range and severity from patient to patient. However, in many individuals with PHS-associated abnormalities may include the presence of extra fingers and/or toes; an abnormal division of the epiglottis (bifid epiglottis); a malformation of the hypothalamus (hypothalamic hamartoma), a portion of the brain that coordinates the function of the pituitary gland and has several other functions; decreased pituitary function; and/or a condition in which a thin covering blocks the anal opening or the passage that normally connects the anus and the lowest part of the large intestine (rectum) fails to develop (imperforate anus). Additional symptoms and findings may include characteristic malformations of the head and facial area and/or other abnormalities. PHS is inherited in an autosomal dominant pattern and is caused by mutations (gene changes) in the GLI3 gene.

Pallister-Hall syndrome is named for Judith Hall and Philip Pallister who described the condition in 1980.


Symptoms and findings in individuals with PHS may vary greatly in range and severity from case to case. Whereas some affected individuals may have only a few characteristic abnormalities, others may have a majority of symptoms and physical features associated with the disorder.

The most common characteristic features of PHS include the presence of extra fingers and/or toes (polydactyly); fusion (osseous syndactyly) of certain fingers and/or toes (digits); and improper development (dysplasia) of the nails. In some cases, the polydactyly associated with PHS may be characterized by the presence of an extra digit between the third and fourth digits (mesoaxial polydactyly) of the hands and/or feet. In other cases, affected individuals may have an extra (supernumerary) digit on the "pinky" (ulnar) side of the hand or the outer (fibular) aspect of the foot (postaxial polydactyly). Many individuals with PHS may also have a condition in which a thin covering blocks the anal opening or the passage that normally connects the anus and the lowest part of the large intestine (rectum) fails to develop (imperforate anus).

According to reports in the medical literature, one of the most significant features of PHS is the presence of a malformation of the hypothalamus (hypothalamic hamartoma), a portion of the brain that coordinates the function of the pituitary gland and that regulates many additional bodily functions. The pituitary gland is the hormone-producing gland at the base of the brain. This is a malformation (and is not a tumor) of the hypothalamus and may cause abnormalities in pituitary function in those who are severely affected. Impaired pituitary function can cause an abnormally small penis (micropenis), low functioning of the thyroid (hypothyroidism), growth hormone deficiency, precious puberty, or more rarely, can cause diabetes or lack of cortisol production. Seizures also commonly result from neurological complications due to hypothalamic hamartoma.

In some infants affected by severe hypothalamic hamartoma, decreased or absent pituitary function (hypopituitarism) may be present at birth. This may lead to low blood sugar (hypoglycemia), abnormal electrolyte levels, and unusually high acid levels in blood and body tissue (metabolic acidosis). Affected individuals may also experience lethargy and an abnormal yellowish discoloration of the skin, mucous membranes, and whites of the eyes (jaundice). Hypopituitarism may result in severe, life-threatening complications without prompt, appropriate treatment. (For more information on hypopituitarism, see the Related Disorders section of this report.)

Infants with PHS may also have distinctive abnormalities of the head and facial (craniofacial) area including unusually small ears that are rotated toward the back of the head; a short nose with upturned nostrils (anteverted nares) and a broad or flat nasal bridge; and/or an unusually long vertical groove in the middle of the upper lip (philtrum). Affected individuals may also have an unusually small tongue (microglossia); an abnormal cleft or fissure in the larynx, the organ in the throat that is involved in voice production and that prevents food from entering the airway during swallowing; and abnormal division of the epiglottis (bifid epiglottis), the flap of cartilage in front of the entrance to the larynx.

In some cases, individuals with PHS may have additional abnormalities. These may include the presence of certain teeth at birth (natal teeth), abnormal folds of movement-limiting mucous membrane tissue in the cheek area of the mouth (buccal frenula), abnormally short arms and/or legs (limbs), and/or dislocated hips. In some affected individuals, additional abnormalities may include abnormal development of the lobes of the lungs, absence (agenesis) and/or improper development (dysplasia) of the kidneys; and/or heart defects that are present at birth (congenital heart defects).
Although most individuals with PHS do not experience life-threatening malformations, some affected individual have an early lethality variant of the disorder. This early lethality is most likely attributable to adrenocortical hormone deficiency caused by the hypothalamic hamartoma or severe airway malformations such as laryngotracheal clefts.


PHS is inherited in an autosomal dominant pattern with wide variability in expression and is caused by mutations in the GLI3 gene. In affected families, most individuals with the familial GLI3 gene mutation will have symptoms and findings associated with the disorder (high penetrance). However, in such cases, the characteristics that are manifested may vary in range and severity from patient to patient. The variability within a particular family appears to be less than the variability in affected members of different families. GLI3 is the only gene known to be associated with PHS, and 95% of affected individuals have an identifiable gene mutation.

The GLI3 gene has been located on the short arm (p) of chromosome 7 (7p13). Chromosomes are found in the nucleus of all body cells. They carry the genetic characteristics of each individual. Pairs of human chromosomes are numbered from 1 through 22, with an unequal 23rd pair of X and Y chromosomes for males, and two X chromosomes for females. Each chromosome has a short arm designated as "p" and a long arm identified by the letter "q". Chromosomes are further subdivided into many bands that are numbered. For example, "chromosome 7p13" refers to band 1 sub-band 3 on the short arm of chromosome 7.

Genetic traits are determined by two genes, one received from the father and one from the mother. Dominant genetic disorders occur when only a single copy of an abnormal gene is sufficient for the appearance of the disease. In the case of PHS, the disease is caused by the presence of one (of the two) copy of GLI3. The abnormal gene can be inherited from either parent, or can be the result of a new mutation in the affected individual. The risk of passing the abnormal gene from the affected parent to offspring is 50% with each pregnancy regardless of the sex of the resulting child.

In a number of patients with PHS, the GLI3 mutation is not inherited from either parent and is instead a new mutation. In general, these patients are more likely to be severely affected than is a child born to an affected parent.

Affected Populations

PHS is an extremely rare disorder that is typically apparent at birth (congenital), appears to affect males and females equally. Approximately 100 patients have been reported in the medical literature, including affected individuals from several large families (kindreds) and isolated cases in which a positive family history has not been found. The range and severity of associated symptoms and findings may vary greatly from case to case (variable expressivity). Because PHS is extremely variable and therefore may be under- or misdiagnosed, it may be difficult to determine the true frequency of the disorder in the general population.

Related Disorders

Symptoms of the following disorders can be similar to those of Pallister-Hall syndrome. Comparisons may be useful for a differential diagnosis:
There are a number of related disorders characterized by mutations in the GLI3 gene. This group of disorders includes Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, postaxial polydactyly type A, and preaxial polydactyly type IV. These disorders occur due to different mutations of the GLI3 gene (allelic disorders) and share some similar characteristics. Despite similarities, these disorders are considered distinct clinical entities.

Greig cephalopolysyndactyly syndrome (GCPS) is a rare inherited disorder characterized by physical abnormalities affecting the fingers and toes (digits) and the head and facial area. Characteristic digital features may include extra fingers and/or toes, webbing and/or fusion of the fingers and/or toes, and/or additional abnormalities. Craniofacial malformations associated with this disorder may include a large and/or unusually shaped skull; a high, prominent forehead (frontal bossing); an abnormally broad nasal bridge; widely spaced eyes (ocular hypertelorism); and/or other physical abnormalities. The range and severity of symptoms may vary greatly from case to case. In most cases, GCPS is inherited as an autosomal dominant trait. For more information on this disorder, choose "Greig Cephalopolysyndactyly Syndrome" as your search term in the Rare Disease Database.

Oral-facial-digital syndrome (OFD) is a rare inherited disorder categorized into types I-IV. Symptoms common to all four types of the syndrome include neuromuscular disturbances, overgrowth of the band of tissue under the tongue (frenulum), extra skin folds at the inner corners of the eyes (epicanthus), broad-based nose, malformations of the hands and feet (i.e., polydactyly or webbing between the fingers and/or toes), extra divisions between the bones of the skull, and/or clefts of the tongue, palate, and/or lip. Other symptoms depend on the form of the syndrome affecting the individual, and may include intellectual disability, extra teeth and/or tooth malformations, and/or eyes that look away from each other (exotropia) or wink involuntarily in an alternating pattern). (For more information on this disorder, choose "Oral- Facial-Digital Syndrome" as your search term in the Rare Disease Database.) Some patients with OFD have GLI3 mutations.

There are several disorders that overlap with PHS but are caused by mutations in other genes.

Holt-Oram syndrome (HOS) is a rare genetic disorder characterized by distinctive malformations of the bones of the thumbs and forearms and/or abnormalities of the heart. The symptoms and physical findings associated with Holt-Oram syndrome may vary greatly from case to case. In many infants with the disorder, the thumbs may be absent or underdeveloped or have an extra bone (triphalangy). Affected infants may also have additional upper limb malformations such as underdevelopment (hypoplasia) of or extra bones in the wrists (e.g., scaphoid bone); malformations of certain bones of the hands (metacarpals); and/or underdevelopment of the bones of the forearms (radius and ulna) and/or the bones of the upper arms (humerus). The shoulder blades (scapulae), the collarbones (clavicles), and/or other bones may also be abnormal. Holt-Oram syndrome is known to be autosomal dominant (For more information on this disorder, choose "Holt-Oram Syndrome" as your search term in the Rare Disease Database.)

McKusick-Kaufman syndrome is a very rare genetic disorder characterized by the presence of a cystic abdominal mass caused by dilation of the vagina and uterus and containing cervical secretions (hydrometrocolpos), abnormalities of the heart and extra well-formed digits on the hands and /or feet (mesoaxial or postaxial polydactyly).

Hydrolethalus syndrome is a very rare developmental disorder characterized by severe brain and/or spinal (central nervous system) malformations and extra fingers and/or toes. Two great toes on each foot, underdeveloped eyes, a small lower jaw, and/or a poorly formed nose are common. The head may be oversized (macrocephaly) with prominent areas on the forehead (frontal) and at the back of the head (occipital). Lung and heart abnormalities may also occur.

Standard Therapies

The diagnosis of PHS is made based on a thorough clinical evaluation, a detailed family history and a variety of specialized tests such as magnetic resonance imaging (MRI) used to detect the presence and dimensions of a hamartoma. Additional tests that may aid in the diagnosis and evaluating the severity of PHS include renal ultrasonography and fiberoptic laryngoscopy. Molecular genetic testing for mutations in the GLI3 gene can confirm the diagnosis and may be especially important in helping to diagnose individuals with more mild presentations of the disorder.

Clinical Testing and Work-Up
The following evaluations may be done to determine the severity of disease in an individual diagnosed with PHS: assessment for cortisol deficiency, consultation by an endocrinologist, cranial MRI to establish the location and extent of hamartoma, neurologic examination, limb X-rays, kidney ultrasound, laryngoscopy to view the epiglottis, surgical consultation if imperforate anus or anal stenosis is present, and a developmental assessment.

Infants with PHS who have decreased or absent pituitary function (hypopituitarism) must be treated immediately with hormonal replacement therapy (i.e., thyroxine, and hydrocortisone). Treatment of hypopituitarism usually resolves the associated symptoms (hypoglycemia, abnormal electrolyte levels, and/or metabolic acidosis). Close monitoring and prompt treatment is imperative to prevent life-threatening complications.

Periodic examinations with specialized equipment to monitor the hypothalamic malformation associated with this disorder are essential. An MRI test is often required since computerized tomography (CT scan) may not always detect hypothalamic hamartomas. Surgical removal of a hamartoma is generally not indicated since it is a malformation and is not a tumor. Surgical removal of extra digits is often performed during infancy.

Seizures may be treated with an anticonvulsant medication such as carbamazepine.
Genetic counseling is recommended for affected individuals and their family members.

Investigational Therapies

Information on current clinical trials is posted on the Internet at All studies receiving U.S. government funding, and some supported by private industry, are posted on this government website.

For information about clinical trials being conducted at the National Institutes of Health (NIH) Clinical Center in Bethesda, MD, contact the NIH Patient Recruitment Office:

Tollfree: (800) 411-1222
TTY: (866) 411-1010

For information about clinical trials sponsored by private sources, contact:

For information about clinical trials conducted in Europe, contact:

A study sponsored by the National Human Genome Research Institute is being conducted to increase understanding of the cause(s) and characteristics of Pallister-Hall syndrome and several related syndromes. For information, contact the NIH Patient Recruitment Office listed above.

Pallister Hall Syndrome Resources

NORD Member Organizations:

(To become a member of NORD, an organization must meet established criteria and be approved by the NORD Board of Directors. If you're interested in becoming a member, please contact Susan Olivo, Membership Manager, at

Other Organizations:


Biesecker LG. The Pallister-Hall and Greig cephalopolysyndactyly syndromes. In: the management of genetic syndromes. Eds. Cassidy SB and Allanson JE, Chapter 41. Wiley Online Library 2010.

Feuillan P, Biesecker LG. Pallister-Hall Syndrome. In: NORD Guide to Rare Disorders. Philadelphia, PA: Lippincott Williams & Wilkins; 2003:230-31.

Buyse ML., ed. Birth Defects Encyclopedia. Dover, MA: Blackwell Scientific Publications; For: The Center for Birth Defects Information Services Inc; 1990:932-4.

Johnston JJ, Sapp JC, Turner JT, et al. Molecular analysis expands the spectrum of phenotypes associated with GLI3 mutations. Hum Mutation. 2010 31:1142-1154

Biesecker LG. What you can learn from one gene: GLI3. J Med Genet 2006 43:465-469

Johnston JJ, Olivos-Glander I, Killoran C, et al. Molecular and clinical analyses of Greig cephalopolysyndactyly and Pallister-Hall syndromes: robust phenotype prediction from the type and position of GLI3 mutations. Am J Hum Genet. 2005;76:609-22.

Boudreau EA, Liow K, Frattali CM, et al. Hypothalamic hamartomas and seizures: distinct natural history of isolated and Pallister-Hall syndrome cases. Epilepsia. 2005;46:42-7.

Feuillan P, Peters KF, Cutler GB Jr, et al. Evidence for decreased growth hormone in patients with hypothalamic hamartoma due to Pallister-Hall syndrome. J Pediatr Endocrinol Metab. 2001;14:141-49.

Killoran CE, Abbott M, McKusick VA, et al. Overlap of PIV syndrome, VACTERL and Pallister-Hall syndrome: clinical and molecular analysis. Clin Genet. 2000;58:28-30.

Kuo JS, Casey SO, Thompson L, et al. Pallister-Hall syndrome: clinical and MR features. AJNR Am J Neuroradiol. 1999;20:1839-41.

Ming JE, Roessler E, Muenke M. Human developmental disorders and the Sonic hedgehog pathway. Mol Med Today. 1998;4:343-39.

Kang S, et al. GL13 frameshift mutations cause autosomal dominant Pallister-Hall syndrome. Nature Genet. 1997;15;266-68.

Biesecker LG, et al. Pallister-Hall syndrome. J Med Genet. 1996;33;585-89.

Biesecker LG, Abbott M, Allen J, et al. Report from the workshop on Pallister-Hall syndrome and related phenotypes. Am J Med Genet .1996;65:76-81.

Biesecker LG. (Updated September 13, 2012) Pallister-Hall Syndrome. In: GeneReviews at GeneTests: Medical Genetics Information Resource (database online). Copyright, University of Washington, Seattle. 1997-2012. Available at Accessed May 9, 2013.

The information in NORD’s Rare Disease Database is for educational purposes only. It should never be used for diagnostic or treatment purposes. If you have questions regarding a medical condition, always seek the advice of your physician or other qualified health professional. NORD’s reports provide a brief overview of rare diseases. For more specific information, we encourage you to contact your personal physician or the agencies listed as “Resources” on this report.

Report last updated: 2013/05/14 00:00:00 GMT+0

0-9 - A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z

NORD's Rare Disease Information Database is copyrighted and may not be published without the written consent of NORD.

Copyright ©2015 NORD - National Organization for Rare Disorders, Inc. All rights reserved.
The following trademarks/registered service marks are owned by NORD: NORD, National Organization for Rare Disorders, the NORD logo, RareConnect. .