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Gene

FOXE1

forkhead box E1

Summary

Cytogenetic location
9q22.33
Coordinates
Chromosome 9: 97,853,226–97,856,717 (GRCh38)
Exons
1 exon across 3.5 kb
Protein
373 amino acids
Also known as
TTF-2, HFKH4
Previous symbols
FKHL15, TITF2, FOXE2
MANE Select transcript
ENST00000375123.5NM_004473.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Congenital Hypothyroidism

    • Bamforth-Lazarus syndromeAutosomal recessive

      Congenital hypothyroidism due to an absent or underdeveloped thyroid with cleft palate and spiky hair, caused by FOXE1 variants.

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

How FOXE1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 9, with a bracket where FOXE1 sits. FOXE1 and 14 genes near it on chromosome 9, from 97,354,972 to 98,354,971.Chromosome 99q22.33p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.397.4 Mb97.6 Mb97.8 Mb98 Mb98.2 MbCCDC180: 97,307,304–97,378,751, forward strandCCDC180TDRD7: 97,411,974–97,496,125, forward strandTDRD7TMOD1: 97,501,180–97,606,817, forward strandTMOD1TSTD2: 97,600,080–97,633,576, reverse strandTSTD2NCBP1: 97,633,402–97,676,992, forward strandNCBP1XPA: 97,653,139–97,697,408, reverse strandXPAFOXE1: 97,853,226–97,856,717, forward strandFOXE1TRMO: 97,894,512–97,922,570, reverse strandTRMOHEMGN: 97,926,791–97,944,856, reverse strandHEMGNANP32B: 97,983,126–98,017,079, forward strandANP32BTRIM14: 98,035,242–98,119,404, reverse strandTRIM14NANS: 98,056,637–98,084,394, forward strandNANSCORO2A: 98,120,975–98,193,206, reverse strandCORO2ATBC1D2: 98,198,999–98,256,427, reverse strandTBC1D2GABBR2: 98,288,087–98,709,739, reverse strandGABBR2Diagram of FOXE1: one exon on the forward strand of chromosome 9Exon 1: 1 known disease-causing siteExon 1: 97,853,226–97,856,717, 3,492 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 3.5 kb of the gene's 3.5 kb; 1,122 of those bases code for the protein.

Sequencing FOXE1

1

position in FOXE1 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 3.5 kb of FOXE1, introns included, not only the 3.5 kb of exons.

Traits linked to FOXE1

The Human Phenotype Ontology lists these as features of the rare conditions FOXE1 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 2026-10-16: 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.). FOXE1 gene: forkhead box E1. Retrieved 17 October 2026, from https://dantelabs.com/genes/foxe1

Vancouver

Dante Labs. FOXE1 gene: forkhead box E1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/foxe1

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