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    GLI3 GLI family zinc finger 3 [ Homo sapiens (human) ]

    Gene ID: 2737, updated on 30-Jun-2024

    Summary

    Official Symbol
    GLI3provided by HGNC
    Official Full Name
    GLI family zinc finger 3provided by HGNC
    Primary source
    HGNC:HGNC:4319
    See related
    Ensembl:ENSG00000106571 MIM:165240; AllianceGenome:HGNC:4319
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PHS; ACLS; GCPS; PAPA; PAPB; PAP-A; PAPA1; PPDIV; GLI3FL; GLI3-190
    Summary
    This gene encodes a protein which belongs to the C2H2-type zinc finger proteins subclass of the Gli family. They are characterized as DNA-binding transcription factors and are mediators of Sonic hedgehog (Shh) signaling. The protein encoded by this gene localizes in the cytoplasm and activates patched Drosophila homolog (PTCH) gene expression. It is also thought to play a role during embryogenesis. Mutations in this gene have been associated with several diseases, including Greig cephalopolysyndactyly syndrome, Pallister-Hall syndrome, preaxial polydactyly type IV, and postaxial polydactyly types A1 and B. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in ovary (RPKM 4.0), endometrium (RPKM 3.1) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See GLI3 in Genome Data Viewer
    Location:
    7p14.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (41960949..42264268, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (42119298..42422619, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (42000547..42276808, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25899 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:41748736-41749935 Neighboring gene INHBA antisense RNA 1 Neighboring gene inhibin subunit beta A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25901 Neighboring gene uncharacterized LOC124901618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:42068797-42069297 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:42105443-42106096 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:42131129-42131824 Neighboring gene NANOG hESC enhancer GRCh37_chr7:42178252-42178762 Neighboring gene VISTA enhancer hs1586 Neighboring gene VISTA enhancer hs111 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 30 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:42232601-42233188 Neighboring gene VISTA enhancer hs1213 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:42261657-42262165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:42267911-42268690 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:42276552-42277533 Neighboring gene uncharacterized LOC105375249 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:42376548-42377052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:42377053-42377557 Neighboring gene Sharpr-MPRA regulatory region 1141 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:42410696-42411895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:42533107-42533607 Neighboring gene uncharacterized LOC105375250

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Greig cephalopolysyndactyly syndrome Compare labs
    Pallister-Hall syndrome Compare labs
    Polydactyly, postaxial, type A1
    MedGen: C4282400 OMIM: 174200 GeneReviews: Not available
    Compare labs
    Polysyndactyly 4
    MedGen: C1868111 OMIM: 174700 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-01-12)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-12)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order.
    EBI GWAS Catalog
    Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9.
    EBI GWAS Catalog
    Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in T cell differentiation in thymus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in alpha-beta T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anterior semicircular canal development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anterior/posterior pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in artery development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in branching involved in ureteric bud morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in camera-type eye morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell differentiation involved in kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in developmental growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic digestive tract development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in embryonic digestive tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic digit morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in embryonic neurocranium morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in forebrain dorsal/ventral pattern formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in forebrain radial glial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in frontal suture morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heart development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hindgut morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in hippocampus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lambdoid suture morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in larynx morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lateral ganglionic eminence cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lateral semicircular canal development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in layer formation in cerebral cortex IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in limb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lung development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mammary gland specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in melanocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in metanephros development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of alpha-beta T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative thymic T cell selection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in neuroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nose morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in odontogenesis of dentin-containing tooth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in oligodendrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in optic nerve morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of alpha-beta T cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of neuroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of protein import into nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein import into nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proximal/distal pattern formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of bone development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sagittal suture morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in smoothened signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in smoothened signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in smoothened signaling pathway involved in dorsal/ventral neural tube patterning IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway involved in spinal cord motor neuron cell fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway involved in ventral spinal cord interneuron specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thymocyte apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in tongue development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in vocalization behavior IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of GLI-SUFU complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in axoneme IEA
    Inferred from Electronic Annotation
    more info
     
    located_in ciliary base TAS
    Traceable Author Statement
    more info
     
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
     
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription repressor complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    transcriptional activator GLI3
    Names
    GLI-Kruppel family member GLI3
    glioma-associated oncogene family zinc finger 3
    oncogene GLI3
    zinc finger protein GLI3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008434.2 RefSeqGene

      Range
      32059..308319
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000168.6NP_000159.3  transcriptional activator GLI3

      See identical proteins and their annotated locations for NP_000159.3

      Status: REVIEWED

      Source sequence(s)
      AA330409, AC005028, AC005158, AI863961, BC113616, BI497308, DA713549
      Consensus CDS
      CCDS5465.1
      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
      Related
      ENSP00000379258.3, ENST00000395925.8
      Conserved Domains (2) summary
      sd00017
      Location:548570
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:562589
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      41960949..42264268 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420208.1XP_047276164.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    2. XM_047420207.1XP_047276163.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    3. XM_047420205.1XP_047276161.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
      Related
      ENSP00000503743.1, ENST00000677605.1
    4. XM_047420209.1XP_047276165.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    5. XM_047420206.1XP_047276162.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
      Related
      ENSP00000502957.1, ENST00000678429.1
    6. XM_017011997.2XP_016867486.1  transcriptional activator GLI3 isoform X2

      UniProtKB/TrEMBL
      A0A7I2V4X9
    7. XM_011515274.3XP_011513576.1  transcriptional activator GLI3 isoform X3

      UniProtKB/TrEMBL
      A0A2R8YGX0, A0A7I2V4X9
      Related
      ENSP00000496377.1, ENST00000479210.1
      Conserved Domains (2) summary
      sd00017
      Location:489511
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:503530
      zf-H2C2_2; Zinc-finger double domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      42119298..42422619 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357916.1XP_054213891.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    2. XM_054357915.1XP_054213890.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    3. XM_054357913.1XP_054213888.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    4. XM_054357917.1XP_054213892.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    5. XM_054357914.1XP_054213889.1  transcriptional activator GLI3 isoform X1

      UniProtKB/Swiss-Prot
      A4D1W1, O75219, P10071, Q17RW4, Q75MT0, Q75MU9, Q9UDT5, Q9UJ39
      UniProtKB/TrEMBL
      A0A7I2V4X9
    6. XM_054357918.1XP_054213893.1  transcriptional activator GLI3 isoform X2

      UniProtKB/TrEMBL
      A0A7I2V4X9
    7. XM_054357919.1XP_054213894.1  transcriptional activator GLI3 isoform X3

      UniProtKB/TrEMBL
      A0A2R8YGX0, A0A7I2V4X9