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Gli3 Gene Detail
Summary
  • Symbol
    Gli3
  • Name
    GLI-Kruppel family member GLI3
  • Synonyms
    Bph, brachyphalangy
  • Feature Type
    protein coding gene
  • IDs
    MGI:95729
    NCBI Gene: 14634
  • Alliance
    genome feature page
  • Transcription Start Sites
    12 TSS
  • Regulated by
    Rr58, Rr59 (2 regulatory regions)
Location &
Maps
more
  • Sequence Map
    Chr13:15638308-15904611 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 13, 5.43 cM, cytoband A2
  • Mapping Data
    37 experiments
Strain
Comparison
more
  • SNPs within 2kb
    7095 from dbSNP Build 142
  • Strain Annotations
    19
  • PCR
    2
  • RFLP
    3
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_95729
 protein coding gene Chr13:15637820-15904611 (+)
129S1/SvImJ ENSMUSG00200013510
 protein coding gene Chr13:12836503-13103753 (+)
A/J ENSMUSG00195037045
 protein coding gene Chr13:11935243-12202083 (+)
AKR/J ENSMUSG00220030942
 protein coding gene Chr13:11929620-12201528 (+)
BALB/cJ ENSMUSG00180032773
 protein coding gene Chr13:12284835-12551659 (+)
C3H/HeJ ENSMUSG00175031122
 protein coding gene Chr13:12386136-12652935 (+)
C57BL/6NJ ENSMUSG00215023190
 protein coding gene Chr13:12393259-12660087 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0018241
 protein coding gene Chr13:10977781-11247560 (+)
CAST/EiJ ENSTCUG00005013480
 protein coding gene Chr13:12511209-12777313 (+)
CBA/J ENSMUSG00210029216
 protein coding gene Chr13:12251750-12518543 (+)
DBA/2J ENSMUSG00185012855
 protein coding gene Chr13:12946512-13213312 (+)
FVB/NJ ENSMUSG00205042878
 protein coding gene Chr13:12158115-12425410 (+)
JF1/MsJ ENSUMUG00000012633
 protein coding gene Chr13:12757419-13029290 (+)
LP/J ENSMUSG00230034751
 protein coding gene Chr13:22355447-22622248 (+)
NOD/ShiLtJ ENSMUSG00190018997
 protein coding gene Chr13:12251615-12518425 (+)
NZO/HlLtJ ENSMUSG00225032096
 protein coding gene Chr13:16140029-16413542 (+)
PWK/PhJ ENSLUMG00010027510
 protein coding gene Chr13:11712368-11978219 (+)
SPRET/EiJ ENSMSPG00010016705
 protein coding gene Chr13:11381872-11648176 (+)
WSB/EiJ ENSIUOG00005032807
 protein coding gene Chr13:11584944-11852162 (+)



Homology
more
  • Human Ortholog
    GLI3, GLI family zinc finger 3
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    GLI3, GLI family zinc finger 3
  • Synonyms
    ACLS, GCPS, GLI3-190, GLI3FL, PAP-A, PAPA, PAPA1, PAPB, PHS, PPDIV
  • Links
    NCBI Gene ID: 2737
    UniProt: P10071

  • Chr Location
    7p14.1; chr7:41960949-42264268 (-)  GRCh38
Human Diseases
more
  • Diseases
    2 with Gli3 mouse models; 6 with human GLI3 associations

Human Disease Mouse Models
      
IDs
 View 1 model
IDs
 View 1 model
      
IDs
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    2 with disease annotations
  • References
    2 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    171 phenotypes from 20 alleles in 33 genetic backgrounds
    185 phenotypes from multigenic genotypes
    4 images
    348 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Homozygous mutants die perinatally with gross polydactyly, multiple craniofacial defects, and frequently, exencephaly. Heterozygotes exhibit enlarged interfrontal bone and extra preaxial digits.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    213
  • GO References
    89
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    2001
  • Tissues
    583
  • cDNA Data
    38
  • Literature Summary
    478
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 14634 NCBI Gene Model | MGI Sequence Detail 266304 C57BL/6J ±  kb
    transcript NM_008130 RefSeq | MGI Sequence Detail 8427 C57BL/6  
    polypeptide Q61602 UniProt | EBI | MGI Sequence Detail 1583 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      7 Sequences
    • Protein Ontology
      PR:000008028 transcriptional activator GLI3
      (term hierarchy)
    • InterPro Domains
      IPR043359 C2H2-type zinc-finger protein GLI-like
      IPR056436 ZIC1-5/GLI1-3like, C2H2 zinc finger
      IPR036236 Zinc finger C2H2 superfamily
      IPR013087 Zinc finger C2H2-type
    • GlyGen
      Q61602 8 sites, 3 N-linked glycans (3 sites), 1 O-linked glycan (4 sites)
    Molecular
    Reagents
    less
    • All nucleic 114
      Genomic 4
      cDNA 46
      Primer pair 25
      Other 39
      Antibodies 33

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGD-MRK-10107, MGD-MRK-1107, MGD-MRK-13222, MGD-MRK-15835, MGD-MRK-1615, MGI:2145311, MGI:2145364
    References
    more
    • Summaries
      All 801
      Developmental Gene Expression 478
      Diseases 2
      Gene Ontology 89
      Phenotypes 348
    • Earliest
      J:12947 Lyon MF, et al., The overall rates of dominant and recessive lethal and visible mutation induced by spermatogonial X-irradiation of mice. Genet Res. 1964;5(3):448-467
    • Latest
      J:387144 Nassar CQ, et al., Microtubule binding protein Togaram1 is required for proper development of mammalian forebrain and neural primary cilia. Dev Biol. 2026 May 31;
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory