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Gene

FOXP3

forkhead box P3

Summary

Cytogenetic location
Xp11.23
Coordinates
Chromosome X: 49,250,438–49,264,710 (GRCh38)
Exons
12 exons across 14.3 kb
Protein
431 amino acids
Inheritance
X-linked recessive
Also known as
JM2, XPID, AIID, PIDX, DIETER, SCURFIN
Previous symbols
IPEX
MANE Select transcript
ENST00000376207.10NM_014009.4
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

  • Autoimmune Disease

    • A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis).

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

  • IPEX Syndrome and Other Tregopathies

    • IPEX syndrome (FOXP3)X-linked recessive

      Immune dysregulation, polyendocrinopathy and enteropathy in boys caused by changes in FOXP3, often starting in infancy.

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

      Immunosuppression and early haematopoietic stem cell transplantation improve outcomes.

Inheritance

X-linked recessive
The change is on the X chromosome, so one copy affects males, who have one X, while females with one are usually carriers. A carrier mother passes it on to each child with a one-in-two chance.

How FOXP3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where FOXP3 sits. FOXP3 and 41 genes near it on chromosome X, from 48,757,574 to 49,757,573.Chromosome XXp11.23p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2848.8 Mb49 Mb49.2 Mb49.4 Mb49.6 MbGLOD5: 48,761,744–48,773,648, forward strandGLOD5GATA1: 48,783,122–48,794,311, forward strandGATA1HDAC6: 48,801,372–48,824,986, forward strandHDAC6ERAS: 48,826,513–48,830,138, forward strandERASPCSK1N: 48,831,088–48,835,632, reverse strandPCSK1NTIMM17B: 48,880,274–48,898,143, reverse strandPQBP1: 48,890,197–48,903,640, forward strandPQBP1SLC35A2: 48,903,180–48,911,958, reverse strandSLC35A2PIM2: 48,913,172–48,919,546, reverse strandPIM2OTUD5: 48,922,024–48,958,390, reverse strandOTUD5KCND1: 48,960,982–48,971,916, reverse strandKCND1GRIPAP1: 48,973,719–49,002,265, reverse strandGRIPAP1TFE3: 49,028,726–49,043,512, reverse strandTFE3CCDC120: 49,053,463–49,073,357, forward strandCCDC120PRAF2: 49,070,107–49,074,022, reverse strandPRAF2: 49,071,470–49,079,887, reverse strandWDR45: 49,074,431–49,101,203, reverse strandWDR45GPKOW: 49,112,941–49,123,750, reverse strandGPKOWMAGIX: 49,162,564–49,169,931, forward strandMAGIXPLP2: 49,171,787–49,175,387, forward strandPLP2PRICKLE3: 49,174,802–49,186,528, reverse strandPRICKLE3SYP: 49,187,807–49,200,218, reverse strandSYPCACNA1F: 49,205,063–49,233,371, reverse strandCCDC22: 49,235,444–49,250,526, forward strandCCDC22FOXP3: 49,250,438–49,264,710, reverse strandFOXP3: 49,258,343–49,270,477, reverse strandPPP1R3F: 49,269,771–49,301,468, forward strandPPP1R3FGAGE10: 49,303,645–49,319,844, forward strandGAGE10GAGE12J: 49,322,037–49,329,387, forward strandGAGE12JGAGE13: 49,331,575–49,338,952, forward strandGAGE13GAGE2E: 49,341,192–49,345,922, forward strandGAGE12B: 49,529,869–49,529,985, forward strandGAGE12BGAGE12C: 49,532,177–49,539,541, forward strandGAGE12CGAGE12D: 49,541,733–49,549,097, forward strandGAGE12DGAGE12E: 49,551,289–49,558,645, forward strandGAGE12EGAGE12F: 49,560,842–49,568,209, forward strandGAGE12G: 49,570,400–49,577,757, forward strandGAGE12H: 49,579,945–49,587,304, forward strandGAGE2A: 49,589,476–49,596,834, forward strandGAGE1: 49,599,020–49,608,538, forward strandGAGE1PAGE1: 49,687,445–49,696,024, reverse strandPAGE1PAGE4: 49,752,516–49,835,255, forward strandPAGE4Diagram of FOXP3: 12 exons on the reverse strand of chromosome XExon 12: 7 known disease-causing sitesExon 11: 4 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 4: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 2: 3 known disease-causing sitesExon 12: 49,250,438–49,251,483, 1,046 basesExon 11: 49,251,664–49,251,765, 102 basesExon 10: 49,253,126–49,253,202, 77 basesExon 9: 49,253,917–49,254,067, 151 basesExon 8: 49,255,429–49,255,509, 81 basesExon 7: 49,255,715–49,255,802, 88 basesExon 6: 49,256,751–49,256,855, 105 basesExon 5: 49,256,925–49,257,012, 88 basesExon 4: 49,257,427–49,257,565, 139 basesExon 3: 49,257,664–49,257,768, 105 basesExon 2: 49,258,296–49,258,527, 232 basesExon 1: 49,264,661–49,264,710, 50 bases1210864215′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 2.3 kb of the gene's 14.3 kb; 1,296 of those bases code for the protein.

How a genome test reads FOXP3

39

positions in FOXP3 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 14.3 kb of FOXP3, introns included, not only the 2.3 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.). FOXP3 gene: forkhead box P3. Retrieved 17 October 2026, from https://dantelabs.com/genes/foxp3

Vancouver

Dante Labs. FOXP3 gene: forkhead box P3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/foxp3

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