GLI3-Related Disorders (GLI3) Sequencing and Deletion/Duplication
Ordering Recommendation

Most comprehensive test to confirm a clinical diagnosis of Pallister-Hall syndrome or Greig cephalopolysyndactyly syndrome.

Polymerase Chain Reaction/ Sequencing/Multiplex Ligation-dependent Probe Amplification
Sun- Sat
14-21 days
New York DOH Approval Status
Specimens from New York clients will be sent out to a New York DOH approved laboratory, if possible.
Specimen Required
Patient Preparation
Lavender (EDTA), pink (K2 EDTA), or Yellow (ACD Solution A or B). 
Specimen Preparation
Transport 3 mL whole blood. (Min: 1 mL) 
Storage/Transport Temperature
Unacceptable Conditions
Ambient: 72 hours; Refrigerated: 1 week; Frozen: Unacceptable 
Reference Interval
Interpretive Data
Background Information for GLI3-Related Disorders (GLI3) Sequencing and Deletion/Duplication:
: Mutations in the GLI3 gene cause multiple disorders. The most common disorders are Pallister-Hall syndrome (PHS) and Greig Cephalopolysyndactyly syndrome (GCPS).
PHS is characterized by hypothalamic hamartoma, postaxial/central polydactyly, and bifid epiglottis. Some individuals may exhibit imperforate anus, renal, genitourinary, pulmonary, or non-polydactyly skeletal anomalies.
GCPS is characterized by preaxial polysyndactyly, hypertelorism, and macrocephaly. Severe cases may exhibit seizures, hydrocephalus, and/or intellectual disability.
Inheritance: Autosomal dominant
Cause: Pathogenic germline mutations in the GLI3 gene.
Clinical sensitivity: PHS - 90 percent; GCPS - 75-85 percent
Methodology: Bidirectional sequencing of the entire coding region and intron/exon boundaries of the GLI3 gene. Multiplex Ligation-dependent Probe Amplification (MLPA) to detect large exonic GLI3 deletions and duplications.
Analytical sensitivity and specificity: Greater than 99 percent for sequencing; greater than 98 percent for MLPA.
Limitations: Diagnostic errors can occur due to rare sequence variations. Regulatory region mutations, deep intronic mutations, and large deletions/duplications are not detected. The breakpoints of large deletions and duplications are not determined. Mutations in genes other than GLI3 are not detected

Counseling and informed consent are recommended for genetic testing. Consent forms are available online at

Statement C: Compliance Statement C: For human genetic inheritable conditions and mutations. This test was developed and its performance characteristics determined by ARUP Laboratories. The U. S. Food and Drug Administration has not approved or cleared this test; however, FDA clearance or approval is not currently required for clinical use. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions.

Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Hotline History
View Hotline History
Component Test Code*Component Chart NameLOINC
2011466GLI3 Seq/DelDup - Specimen31208-2
2011467GLI3 Seq/DelDup - Interpretation35474-6
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please view this test within the Laboratory Test Directory found at
  • Greig Cephalopolysyndactyly syndrome (GCPS)
  • Pallister-Hall syndrome (PHS)
  • polydactyly