The baby’s physical examination revealed distinctive craniofacial features, including a depressed nasal bridge, bilateral infraorbital creases, a thin vermilion border, microretrognathia, and hirsutism. Her skeletal findings were even more telling: rhizomelic shortening of both the upper and lower limbs, syndactyly fusing the fourth and fifth digits of her right hand, and mesoaxial polydactyly on the left, meaning an extra finger had grown in the middle of her hand rather than along its edges. Additional congenital anomalies included a high-arched palate, isolated right choanal atresia, a blockage of the nasal passage that required nasopharyngoscopy to detect, and an imperforate anus with a rectovaginal fistula that necessitated a loop colostomy on day 5 of life.

Imaging studies deepened the clinical mystery. Echocardiography revealed an ostium secundum atrial septal defect, a hole in the wall separating the heart’s two upper chambers. Abdominal ultrasonography demonstrated a solitary left kidney, with complete agenesis of the right kidney and no adrenal tissue visualized in the right renal fossa. But the most consequential finding came from brain magnetic resonance imaging, which identified a large, non-enhancing exophytic lesion arising from the tuber cinereum, a region at the base of the hypothalamus. Measuring 5.0 by 3.4 by 3.2 centimeters, the mass extended into the prepontine, interpeduncular, and suprasellar cisterns, exerting mass effect on the brainstem, displacing the optic chiasm superiorly, and compressing the pituitary stalk. This was a hypothalamic hamartoma, a benign but strategically located growth of disorganized neural tissue.

The combination of a hypothalamic hamartoma and mesoaxial polydactyly is the defining signature of Pallister-Hall syndrome, a rare autosomal dominant disorder caused by variants in the GLI3 gene. First linked to GLI3 frameshift mutations in 1997, the syndrome takes its name from the gene’s role as a zinc-finger transcription factor in the Sonic Hedgehog signaling pathway, a master regulator of embryonic limb and central nervous system development. The gene occupies a peculiar position in medical genetics: truncating variants in the middle third of its coding sequence, roughly open reading frame nucleotides 1998 through 3481, most often produce Pallister-Hall syndrome, while variants that simply reduce the amount of functional protein, a mechanism called haploinsufficiency, more commonly cause a different condition entirely, Greig cephalopolysyndactyly syndrome. The relationship is strong but not absolute, and exceptions on both sides have been documented.

Whole-exome sequencing was performed at an external clinical laboratory using the xGen Exome Research Panel v2.0 combined with the xGen Human mtDNA Research Panel v1.0 from Integrated DNA Technologies, followed by sequencing on an Illumina NovaSeq X instrument. Secondary analysis used DRAGEN against the hg38 human reference genome, with tertiary analysis on the Geneyx Analysis platform. The assay achieved a mean target coverage of 195.8-fold, with 95.35 percent of targeted bases covered at least 20-fold, well above the thresholds typically required for confident variant calling. The analysis identified a heterozygous GLI3 variant, NM_000168.6:c.2410del, which produces a frameshift beginning at amino acid 804 and predicted to truncate the protein five residues downstream as p.Val804SerfsTer5. The variant was absent from gnomAD v4.1, the largest public database of human genetic variation, and from ClinVar, the clinical variant archive, at the time of analysis in December 2025.

Sanger sequencing, a targeted confirmation method, verified the variant in the proband and demonstrated its absence in both parents and in her 4-year-old brother, supporting a presumed de novo origin, meaning the mutation arose spontaneously in the child rather than being inherited. The frameshift begins downstream of the zinc-finger domain, squarely within the middle-third PHS-associated region. The variant was provisionally classified as likely pathogenic using American College of Medical Genetics and Genomics criteria, specifically PM1, PM6, PM2_supporting, and PP4. Notably, the strongest criterion for loss-of-function variants, PVS1, was deliberately not applied, because Pallister-Hall syndrome is associated with a location-specific truncated-repressor mechanism rather than conventional loss of function. In other words, the disease mechanism depends not simply on losing GLI3 function but on where along the gene the truncation occurs, a subtlety that separates sophisticated variant interpretation from rote application of guidelines.

The differential diagnosis had initially pointed elsewhere. The combination of anorectal, cardiac, renal, and limb anomalies raised consideration of VACTERL association, a non-random clustering of vertebral, anal, cardiac, tracheoesophageal, renal, and limb defects. But VACTERL does not typically include hypothalamic hamartoma or mesoaxial polydactyly, and the co-occurrence of these two cardinal findings strongly favored Pallister-Hall syndrome. Greig cephalopolysyndactyly syndrome was considered and set aside because it typically features macrocephaly, hypertelorism, and preaxial polydactyly, with hypothalamic hamartoma not being characteristic. Other GLI3-related disorders, oral-facial-digital syndromes, and ciliopathies were similarly weighed and excluded based on the specific constellation of findings and the position of the truncating variant.

One element of the family history demanded careful interpretation. The proband’s 4-year-old brother had been diagnosed with a choroid plexus papilloma, a rare tumor of the brain’s cerebrospinal fluid-producing tissue, and treated with ventriculoperitoneal shunting. Sanger sequencing confirmed that he did not carry the GLI3 variant identified in his sister. In the absence of a shared variant or an established association between GLI3-related Pallister-Hall syndrome and choroid plexus papilloma, the sibling’s tumor is considered most likely incidental, a conclusion that spares the family unnecessary anxiety about inherited cancer risk.

Comparing this case with regional and molecularly relevant reports reveals both patterns and puzzles. A Saudi Arabian patient carrying a nearby variant, NM_000168.5:c.2396dup predicted as p.Lys800Ter, also had hypothalamic hamartoma and polydactyly, but developed gelastic seizures, the characteristic laughing fits of hypothalamic hamartomas, at 13 months, along with central precocious puberty during infancy and subsequent central hypothyroidism. A Lebanese clinical case combined hypothalamic hamartoma and polydactyly with orofacial narrowing and tethered cord, though no patient-specific molecular variant was reported. In an Iranian family, a homozygous c.1927C>T variant producing p.Arg643Ter was associated with a broad, severe PHS-like phenotype in a fetus, while heterozygous relatives had only polydactyly, suggesting an effect of allelic dosage. Larger molecular series reinforce the location-dependent association: the variant c.2385del, producing p.Ile796fsTer13, was reported in Pallister-Hall syndrome near the position affected in the present patient, while c.2374C>T, producing p.Arg792Ter, represents a documented Greig cephalopolysyndactyly exception within the PHS-associated region. In the Démurger cohort of 76 individuals from 55 families, renal anomalies occurred in 41 percent of evaluable PHS cases, ranging from hypoplasia to agenesis, indicating that the present patient’s right renal agenesis falls within recognized syndrome variability rather than establishing a novel association.

At the last documented assessment, the patient was 89 days old, clinically stable, and had shown no seizures and no biochemical evidence of pituitary dysfunction. Baseline endocrine evaluation, including free thyroxine, thyroid-stimulating hormone, growth hormone, and gonadotropins, had yielded values within age-appropriate reference ranges. Yet the authors are careful to note that the absence of seizures or endocrine dysfunction at this early age cannot predict later outcome, because these manifestations may emerge with time. Ongoing surveillance includes neurological and developmental assessment, monitoring of growth and pubertal development, age-appropriate pituitary testing, and neuroimaging as directed by the treating team. The case adds variant-level evidence to the global GLI3 literature and demonstrates a principle that extends far beyond a single patient: molecular position, clinical phenotype, and the age at which a patient is assessed must all be interpreted together before drawing conclusions about genotype-phenotype relationships in rare disease.

Subject of Research: A de novo GLI3 frameshift variant causing Pallister-Hall syndrome in a Palestinian infant

Article Title: Case Report: Pallister-Hall syndrome associated with a previously unreported de novo GLI3 frameshift variant and diagnostic insights from the Middle East

Article References: Khalil, G., Hemieid, I. K., & Malki, E. G. (2026). Case Report: Pallister-Hall syndrome associated with a previously unreported de novo GLI3 frameshift variant and diagnostic insights from the Middle East. Frontiers in Pediatrics, 14, Article 1818628. https://doi.org/10.3389/fped.2026.1818628

Image Credits: AI Generated

DOI: 10.3389/fped.2026.1818628

Keywords: Pallister-Hall syndrome, GLI3, hypothalamic hamartoma, polydactyly, whole-exome sequencing, de novo variant, genetics, rare disease, Middle East, pediatrics, Sonic Hedgehog pathway, genotype-phenotype correlation