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Gene

FOXC1

forkhead box C1

Summary

Cytogenetic location
6p25.3
Coordinates
Chromosome 6: 1,609,915–1,613,897 (GRCh38)
Exons
1 exon across 4 kb
Protein
553 amino acids
Inheritance
Autosomal dominant
Also known as
FREAC3, ARA, IGDA, IHG1
Previous symbols
FKHL7, IRID1
MANE Select transcript
ENST00000645831.2NM_001453.3
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 reports relevant to this gene

  • Anterior Segment Dysgenesis, Axenfeld-Rieger Syndrome & Aniridia

    • Axenfeld-Rieger SyndromeAutosomal dominant

      A dominant condition caused by changes in PITX2 or FOXC1, affecting the iris and drainage angle and sometimes the teeth, face and navel.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Lifelong glaucoma surveillance is recommended, as about half of affected people develop glaucoma.

    • Anterior Segment Dysgenesis

      A group of developmental conditions of the front of the eye, including Peters anomaly, caused by changes in genes such as FOXC1, PITX3, FOXE3, CYP1B1 and CPAMD8.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      There is a high lifetime risk of glaucoma, so regular eye-pressure monitoring is recommended.

  • Glaucoma

    • Increased pressure in the eyeball due to obstruction of the outflow of aqueous humor.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      IOP-lowering drops (prostaglandin analogs, beta-blockers); selective laser trabeculoplasty; MIGS surgery; trabeculotomy/goniotomy for congenital glaucoma; cascade family genetic testing; annual IOP monitoring for carriers

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How FOXC1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where FOXC1 sits. FOXC1 and 3 genes near it on chromosome 6, from 1,111,906 to 2,111,905.Chromosome 66p25.3p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q271.2 Mb1.4 Mb1.6 Mb1.8 Mb2 MbFOXQ1: 1,312,098–1,314,758, forward strandFOXQ1FOXF2: 1,389,555–1,395,603, forward strandFOXF2FOXC1: 1,609,915–1,613,897, forward strandFOXC1GMDS: 1,622,884–2,245,711, reverse strandGMDSDiagram of FOXC1: one exon on the forward strand of chromosome 6Exon 1: 109 known disease-causing sitesExon 1: 1,609,915–1,613,897, 3,983 bases15′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 4 kb of the gene's 4 kb; 1,662 of those bases code for the protein.

How a genome test reads FOXC1

109

positions in FOXC1 where ClinVar classes a change as pathogenic or likely pathogenic

4 of them (3.7%) fall in regions short reads find hard.

  • Low mappability (4 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 4 kb of FOXC1, introns included, not only the 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.). FOXC1 gene: forkhead box C1. Retrieved 17 October 2026, from https://dantelabs.com/genes/foxc1

Vancouver

Dante Labs. FOXC1 gene: forkhead box C1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/foxc1

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