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Gene

FOXC2

forkhead box C2

Summary

Cytogenetic location
16q24.1
Coordinates
Chromosome 16: 86,566,829–86,569,728 (GRCh38)
Exons
1 exon across 2.9 kb
Protein
501 amino acids
Inheritance
Autosomal dominant
Also known as
MFH-1
Previous symbols
FKHL14
MANE Select transcript
ENST00000649859.1NM_005251.3
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 report relevant to this gene

  • Primary Lymphoedema & Lymphatic Malformations

    • Lymphoedema-Distichiasis SyndromeAutosomal dominant

      A condition caused by changes in FOXC2 that causes leg swelling from puberty and an extra row of eyelashes, sometimes with varicose veins, droopy eyelids or heart defects.

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

      Knowing about it supports compression therapy and eye and heart checks.

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 FOXC2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where FOXC2 sits. FOXC2 and 3 genes near it on chromosome 16, from 86,068,279 to 87,068,278.Chromosome 1616q24.1p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.386.2 Mb86.4 Mb86.6 Mb86.8 Mb87 MbFOXF1: 86,509,697–86,515,422, forward strandFOXF1MTHFSD: 86,530,178–86,555,235, reverse strandMTHFSDFOXC2: 86,566,829–86,569,728, forward strandFOXC2FOXL1: 86,576,340–86,583,478, forward strandFOXL1Diagram of FOXC2: one exon on the forward strand of chromosome 16Exon 1: 23 known disease-causing sitesExon 1: 86,566,829–86,569,728, 2,900 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 2.9 kb of the gene's 2.9 kb; 1,506 of those bases code for the protein.

How a genome test reads FOXC2

23

positions in FOXC2 where ClinVar classes a change as pathogenic or likely pathogenic

3 of them (13%) fall in regions short reads find hard.

  • Low mappability (3 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 2.9 kb of FOXC2, introns included, not only the 2.9 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.). FOXC2 gene: forkhead box C2. Retrieved 16 October 2026, from https://dantelabs.com/genes/foxc2

Vancouver

Dante Labs. FOXC2 gene: forkhead box C2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/foxc2

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