GLI3-related Disorders (GLI3) Deletion/Duplication (INACTIVE as of 05/15/17: Refer to 2011465)
Ordering Recommendation

This is a second-tier test and REQUIRES APPROVAL from ARUP's Genetic Counselor (800-242-2787 x2141) before ordering. Preferred initial test is the sequencing and deletion/duplication test.

Multiplex Ligation-dependent Probe Amplification
Within 14 days
New York DOH Approval Status
Specimens from New York clients will be sent out to a New York DOH approved laboratory, if possible.
ARUP Consult®
Disease Topics
Specimen Required
Patient Preparation
Lavender (EDTA), pink (K2EDTA), or yellow (ACD Solution A or B). 
Specimen Preparation
Transport 3 mL whole blood. (Min: 2 mL) 
Storage/Transport Temperature
Unacceptable Conditions
Ambient: 72 hours; Refrigerated: 1 week; Frozen: Unacceptable 
Reference Interval
By report
Interpretive Data
Background information for GLI3-Related Disorders (GLI3) Deletion/Duplication
: Mutations in the GLI3 gene cause multiple disorders. The most common disorders are Pallister-Hall syndrome (PHS) and Greig Cephalopolysyndactyly syndrome (GCPS).
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.
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-unknown; GCPS-5-10 percent
Methodology: Multiplex ligation-dependent probe amplification (MLPA) to detect large exonic GLI3 deletions and duplications.
Analytical sensitivity and specificity: Greater than 98 percent.
Limitations: Diagnostic errors can occur due to rare sequence variations. Single base pair substitutions, small deletions/duplications, regulatory region mutations, and deep intronic mutations are not detected. The breakpoints of large deletions/duplications are not determined.

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

Compliance Statement C: The performance characteristics of this test were validated by ARUP Laboratories. The U.S. Food and Drug Administration (FDA) has not approved or cleared this test. However, FDA approval or clearance is currently not required for clinical use of this test. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions. ARUP is authorized under Clinical Laboratory Improvement Amendments (CLIA) and by all states to perform high-complexity testing. Counseling and informed consent are recommended for genetic testing. Consent forms are available online.

Component Test Code*Component Chart NameLOINC
2011425GLI3-Related Disorders DelDup - Specimen31208-2
2011426GLI3-Related Disorders DelDup - Interp35474-6
* 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 click the sidebar link to access the Interface Map.
  • Greig Cephalopolysyndactyly syndrome (GCPS)
  • Pallister-Hall syndrome (PHS)
  • Polydactyly