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Gene

GLI3

GLI family zinc finger 3

Summary

Cytogenetic location
7p14.1
Coordinates
Chromosome 7: 41,960,949–42,237,209 (GRCh38)
Exons
15 exons across 276.3 kb
Protein
1,580 amino acids
Also known as
PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV
Previous symbols
GCPS, PHS
MANE Select transcript
ENST00000395925.8NM_000168.6
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Non-Acquired Combined Pituitary Hormone Deficiency

    • Congenital hypopituitarism is characterized by multiple pituitary hormone deficiency, including somatotroph, thyrotroph, lactotroph, corticotroph or gonadotroph deficiencies, due to mutations of pituitary transcription factors involved in pituitary ontogenesis.

      • 5 GenCC submitters rate it definitive or strong

How GLI3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 7, with a bracket where GLI3 sits. GLI3 and 1 gene near it on chromosome 7, from 41,599,079 to 42,599,078.Chromosome 77p14.1p22.3p22.2p22.1p21.3p21.2p21.1p15.3p15.2p15.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.21q11.22q11.23q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q31.1q31.2q31.31q31.32q31.33q32.1q32.2q32.3q33q34q35q36.1q36.2q36.341.6 Mb41.8 Mb42 Mb42.2 Mb42.4 MbINHBA: 41,667,168–41,705,834, reverse strandINHBAGLI3: 41,960,949–42,237,209, reverse strandGLI3Diagram of GLI3: 15 exons on the reverse strand of chromosome 7Exon 15: 56 known disease-causing sitesExon 14: 6 known disease-causing sitesExon 13: 11 known disease-causing sitesExon 12: 6 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 7: 5 known disease-causing sitesExon 6: 3 known disease-causing sitesExon 5: 7 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 2: 2 known disease-causing sitesExon 15: 41,960,949–41,966,641, 5,693 basesExon 14: 41,967,596–41,967,923, 328 basesExon 13: 41,972,337–41,972,627, 291 basesExon 12: 41,977,558–41,977,722, 165 basesExon 11: 41,978,599–41,978,748, 150 basesExon 10: 42,023,468–42,023,608, 141 basesExon 9: 42,025,264–42,025,377, 114 basesExon 8: 42,026,199–42,026,412, 214 basesExon 7: 42,040,038–42,040,239, 202 basesExon 6: 42,045,384–42,045,530, 147 basesExon 5: 42,048,491–42,048,696, 206 basesExon 4: 42,076,752–42,076,857, 106 basesExon 3: 42,148,226–42,148,468, 243 basesExon 2: 42,223,130–42,223,295, 166 basesExon 1: 42,236,971–42,237,209, 239 bases1510515′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 8.4 kb of the gene's 276.3 kb; 4,743 of those bases code for the protein.

How a genome test reads GLI3

122

positions in GLI3 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 276.3 kb of GLI3, introns included, not only the 8.4 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). GLI3 gene: GLI family zinc finger 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/gli3

Vancouver

Dante Labs. GLI3 gene: GLI family zinc finger 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/gli3

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