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Pallister-Hall syndrome (PHS), a pleiotropic autosomal dominant malformative disorder, is characterized by hypothalamic hamartoma, pituitary dysfunction, bifid epiglottis, polydactyly, and, more rarely, renal abnormalities and genitourinary malformations.
Data assembled from 7 of 12 sources · Last updated Oct 4, 2026, 1:08 AM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Common questions about Pallister-Hall syndrome
Organ System | Phenotype Count | Example Features |
|---|---|---|
Arms and legs | 9 | Preaxial hand polydactyly, Toe syndactyly, Preaxial foot polydactyly |
Hormones | 5 | Adrenal hypoplasia, Decreased circulating cortisol level, Precocious puberty |
Growth and development | 4 | Short stature, Decreased response to growth hormone stimulation test, Intrauterine growth retardation |
Kidneys and urinary system | 4 | Renal hypoplasia, Ectopic kidney, Renal dysplasia |
Brain and nerves | 4 | Seizure, Intellectual disability, Global developmental delay |
Head and neck | 4 | Midline facial capillary hemangioma, Cleft palate, Cleft upper lip |
Lungs and breathing | 1 | Abnormal lung lobation |
Lab test results | 1 | Decreased circulating cortisol level |
Skin | 1 | Nail dysplasia |
Heart and blood vessels | 1 | Ventricular septal defect |
GLI3-related Pallister-Hall syndrome (GLI3-PHS) displays a wide range of severity. The literature frequently reflects the assumption that GLI3-PHS is severe and Greig cephalopolysyndactyly syndrome (GCPS) is mild. This assumption is incorrect, as a minority of individuals with GLI3-PHS show multiple severe anomalies and most individuals with GLI3-PHS are mildly affected with polydactyly, asymptomatic bifid epiglottis, and hypothalamic hamartoma. Without careful clinical evaluation, these individuals may be incorrectly diagnosed with postaxial polydactyly type A (PAP-A). Table 2. GLI3-Related Pallister-Hall Syndrome: Frequency of Select Features
Feature | Frequency of Feature1 | Comment |
|---|---|---|
Hypothalamic hamartoma | +++ | — |
Polydactyly | +++ | Postaxial or mesoaxial |
Epiglottis abnormalities | ++ | — |
Behavioral manifestations | + | — |
Genitourinary anomalies | + | — |
Pulmonary segmentation anomalies | + | — |
Imperforate anus | + | — |
Oligodactyly | + | +++ = common; ++ = seen in many affected persons; + = seen in some or a few affected persons Even these coarse estimates of the frequency of specific features are likely to be heavily skewed by phenotypic ascertainment bias. |
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
GLI3 encodes GLI family zinc finger 3 (1,580 aa). Has a dual function as a transcriptional activator and a repressor of the sonic hedgehog (Shh) pathway, and plays a role in limb development. Highest expression in Uterus (27.0 TPM) and Colon Sigmoid (21.9 TPM).
Pallister-Hall syndrome is associated with mutations in the GLI3 gene on chromosome 7.
GLI3 is classified as a druggable target (Transcription Factor category) with score 6.5.
The mutational spectra of GCPS and GLI3-PHS are mostly distinct . GCPS is caused by pathogenic variants of all types, whereas GLI3-PHS is overwhelmingly caused by truncating variants that generate a frameshift and a truncation. Within the frameshift variant category, a genotype-phenotype correlation has been demonstrated on two levels:
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
No instances of incomplete penetrance of GLI3-PHS have been published. reported one individual with apparent germline mosaicism without evident clinical features.
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
Consensus clinical diagnostic criteria for GLI3-related Pallister-Hall syndrome (GLI3-PHS) have been published .
GLI3-PHS should be suspected in individuals with the following features:
Hypothalamic hamartoma, a non-enhancing mass in the floor of the third ventricle posterior to the optic chiasm that is isointense to gray matter on T1- and T2-weighted pulse sequences of an MRI, but may have distinct intensity on FLAIR
Note: Neither cranial CT examination nor cranial ultrasound examination is adequate for diagnosis of hypothalamic hamartoma.
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
Central polydactyly • Oral-facial-digital syndrome type 6 (OMIM 277170), caused by biallelic pathogenic variants in CPLANE1, includes central polydactyly with hypoplasia of the cerebellar vermis. Renal agenesis and dysplasia have been described. • Holzgreve syndrome (OMIM 236110) includes central polydactyly, cleft palate, and heart defect. Postaxial polydactyly. See . Table 4. Disorders Associated with Postaxial Polydactyly in the Differential Diagnosis of GLI3-Related Pallister-Hall Syndrome
Gene | Disorder | MOI | Clinical Features | Comment |
|---|---|---|---|---|
≥26 genes incl:ARL6BBS1BBS2BBS4BBS5BBS7BBS9BBS10BBS12CEP290CFAP418MKKSSDCCAG8TTC8 | Bardet-Biedl syndrome (BBS) |
Genetic testing for GLI3 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for Pallister-Hall syndrome has been reported in the published literature.
No approved treatments are currently available for Pallister-Hall syndrome. The disease remains an area of unmet medical need.
Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with GLI3-related Pallister-Hall syndrome (GLI3-PHS), the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended. Table 5. Recommended Evaluations Following Initial Diagnosis in Individuals with GLI3-Related Pallister-Hall Syndrome
System/Concern | Evaluation | Comment |
|---|---|---|
Behavioral | Neuropsychiatric eval | For persons age 12 mos: screening for concerns incl sleep disturbances, ADHD, anxiety, /or findings suggestive of ASD |
Development | Developmental assessment | To incl motor, adaptive, cognitive, speech-language eval; Eval for early intervention/ special education Genitourinary |
anomalies | Renal ultrasonography to evaluate for renal anomalies | — |
Imperforate anus | Surgical consultation for imperforate anus or anal stenosis if present | Genetic |
counseling | By genetics professionals1 | To inform affected persons their families re nature, MOI, implications of GLI3-PHS to facilitate medical personal decision making Family support resources |
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
Biopsy or resection of hypothalamic hamartoma may result in complications and lifelong need for hormone replacement. Some stimulants (commonly used for attention-deficit/hyperactivity disorder) may exacerbate seizures.
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
View trials for Pallister-Hall syndrome
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the following evaluations are recommended.
Table 7.
Recommended Surveillance for Individuals with GLI3-Related Pallister-Hall Syndrome
System/Concern | Evaluation | Frequency
| • Assess growth.
Monitor for signs of precocious puberty.
| Annually throughout childhood
| Monitor developmental progress educational needs.
| Behavioral assessment
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
Phenotype severity distribution: 1 always present feature, 4 very common features, 6 common features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for Pallister-Hall syndrome.
129 publications have been identified in PubMed for Pallister-Hall syndrome. Research spans Review / Meta-Analysis (64%), Basic Science / Preclinical (15%), and Case Report / Case Series (9%).
Research Type | Count | % of Total |
|---|---|---|
Research summaries | 83 | 64% |
Laboratory research | 19 | 15% |
Patient case studies | 12 | 9% |
Disease patterns and progression | 10 | 8% |
Other research | 3 | 2% |
Testing and diagnosis research | 2 | 2% |
Amado C (2026). [PMID: 40975490](https://pubmed.ncbi.nlm.nih.gov/40975490/). *Ann Allergy Asthma Immunol*. [Review / Meta-Analysis]
Anderson EN (2026). [PMID: 41468891](https://pubmed.ncbi.nlm.nih.gov/41468891/). *Am J Hum Genet*. [Basic Science / Preclinical]
Ferri C (2026). [PMID: 41798958](https://pubmed.ncbi.nlm.nih.gov/41798958/). *Front Immunol*. [Review / Meta-Analysis]
Kanjilal S (2026). [PMID: 40910774](https://pubmed.ncbi.nlm.nih.gov/40910774/). *Oper Neurosurg*. [Case Report / Case Series]
Damião SQ (2026). [PMID: 42166346](https://pubmed.ncbi.nlm.nih.gov/42166346/). *Radiographics*. [Other]
Lee S (2026). [PMID: 41206258](https://pubmed.ncbi.nlm.nih.gov/41206258/). *Am J Geriatr Psychiatry*. [Review / Meta-Analysis]
Papazachariou A (2026). [PMID: 41128447](https://pubmed.ncbi.nlm.nih.gov/41128447/). *Curr Opin Clin Nutr Metab Care*. [Review / Meta-Analysis]
Cornejo-Sanchez DM (2025). [PMID: 40055553](https://pubmed.ncbi.nlm.nih.gov/40055553/). *Eur J Hum Genet*. [Basic Science / Preclinical]
Selikhova M (2025). [PMID: 39991987](https://pubmed.ncbi.nlm.nih.gov/39991987/). *Mov Disord Clin Pract*. [Diagnostic / Biomarker]
Borojeni S (2025). [PMID: 40546148](https://pubmed.ncbi.nlm.nih.gov/40546148/). *Rev Prat*. [Review / Meta-Analysis]
Primarily characterized by retinal cone-rod dystrophy, obesity related complications, postaxial polydactyly, cognitive impairment, hypogonadotropic hypogonadism /or genitourinary malformations, renal malformations /or renal parenchymal disease |
Overall, BBS is much more common than PHS. It is possible that atypical BBS that resembles PHS may be more common than GLI3-related PHS. BBS-related genes should be evaluated in persons w/overlapping findings. |
DHCR7 | Smith-Lemli-Opitz syndrome (SLOS) | AR | Characterized by prenatal postnatal growth restriction, microcephaly, moderate-to-severe ID, multiple major minor malformations (incl postaxial polydactyly 2-3 syndactyly of toes). SLOS is caused by an abnormality in cholesterol metabolism. | — |
MKKS | McKusick-Kaufman syndrome (MKS) | AR | Triad of hydrometrocolpos in females genital malformations in males, PAP or central polydactyly, CHD | Most non-Amish persons w/MKS evolve into the BBS phenotype in older childhood or adulthood. |
SMO | SMO-related hypothalamic hamartoma-polydactyly (OMIM 241800) | AR | Hypothalamic hamartomas w/variable degrees types of polydactyly | Some persons w/this disorder may be properly considered to have SMO-related PHS. |
TBX5 | Holt-Oram syndrome (HOS) | AD | Upper-limb defects, CHD, cardiac conduction disease. Upper-limb malformations may be unilateral, bilateral/symmetric, or bilateral/asymmetric range from triphalangeal or absent thumb(s) to phocomelia. | AD = autosomal dominant; AR = autosomal recessive; CHD = congenital heart disease; ID = intellectual disability; MOI = mode of inheritance; PAP = postaxial polydactyly; PHS = Pallister-Hall syndrome 1. Hypothalamic hamartoma. |
Source: GeneReviews — "GLI3-Related Pallister-Hall Syndrome"
Treatment of Manifestations in Individuals with GLI3-Related Pallister-Hall Syndrome Manifestation/Concern | Treatment | Considerations/Other |
Endocrine | Endocrine abnormalities are treated as in general population, w/treatment for cortisol deficiency being most urgent. | — |
Neurologic | Only under most unusual circumstances should HH be removed or even biopsied because complications of surgery need for lifelong hormone supplements postoperatively generally outweigh benefits. | Seizures are treated symptomatically. |