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Gene

FOXL2

forkhead box L2

Summary

Cytogenetic location
3q22.3
Coordinates
Chromosome 3: 138,944,224–138,947,137 (GRCh38)
Exons
1 exon across 2.9 kb
Protein
376 amino acids
Also known as
BPES1
Previous symbols
BPES
MANE Select transcript
ENST00000648323.1NM_023067.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Female Infertility

    • Diminished or absent ability of a female to achieve conception.

      • 4 GenCC submitters rate it definitive or strong

How FOXL2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 3, with a bracket where FOXL2 sits. FOXL2 and 10 genes near it on chromosome 3, from 138,445,681 to 139,445,680.Chromosome 33q22.3p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29138.6 Mb138.8 Mb139 Mb139.2 Mb139.4 MbESYT3: 138,434,570–138,481,686, forward strandESYT3CEP70: 138,494,339–138,594,538, reverse strandCEP70FAIM: 138,608,550–138,633,643, forward strandFAIMPIK3CB: 138,652,336–138,834,964, reverse strandPIK3CBFOXL2: 138,944,224–138,947,137, reverse strandFOXL2FOXL2NB: 138,947,177–138,953,990, forward strandFOXL2NBPRR23A: 139,003,962–139,006,268, reverse strandPRR23AMRPS22: 139,005,806–139,360,497, forward strandMRPS22PRR23B: 139,019,031–139,020,926, reverse strandPRR23BPRR23C: 139,042,102–139,044,892, reverse strandPRR23CCOPB2: 139,353,942–139,389,736, reverse strandCOPB2Diagram of FOXL2: one exon on the reverse strand of chromosome 3Exon 1: 69 known disease-causing sitesExon 1: 138,944,224–138,947,137, 2,914 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; 1,131 of those bases code for the protein.

Sequencing FOXL2

10Moderate

How hard FOXL2 is to sequence with short reads, out of 100

  • Mappability0%
  • Homology0%
  • Repeats15%
  • GC content77%
  • Reference coverage0%

69

positions in FOXL2 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 2.9 kb of FOXL2, introns included, not only the 2.9 kb of exons.

Genes linked to the same conditions

Traits linked to FOXL2

The Human Phenotype Ontology lists these as features of the rare conditions FOXL2 can cause. Each trait's page lists the other genes linked to it.

External links

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 2026-10-17: 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 Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.18-e609d43e.

Cite this page

APA

Dante Labs. (n.d.). FOXL2 gene: forkhead box L2. Retrieved 18 October 2026, from https://dantelabs.com/genes/foxl2

Vancouver

Dante Labs. FOXL2 gene: forkhead box L2 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/foxl2

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