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Gene

FOXN1

forkhead box N1

Summary

Cytogenetic location
17q11.2
Coordinates
Chromosome 17: 28,506,348–28,538,900 (GRCh38)
Exons
9 exons across 32.6 kb
Protein
648 amino acids
Inheritance
Autosomal recessive
Also known as
FKHL20
Previous symbols
WHN, RONU
MANE Select transcript
ENST00000579795.6NM_001369369.1
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

  • Severe Combined Immunodeficiency

    • Autosomal recessive

      Severe combined immunodeficiency (SCID) comprises a group of rare monogenic primary immunodeficiency disorders characterized by a lack of functional peripheral T lymphocytes resulting in early-onset severe respiratory infections and failure to thrive. They are classified according to immunological phenotype into SCID with absence of T cells but presence of B cells (T-B+ SCID) or SCID with absence of both (T-B- SCID). Both of these groups include several forms, with or without natural killer (NK) cells.

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

Broader groupings

  • Other Inborn Errors of Immunity

    • Immunodeficiency Disease

      One of 170 genes linked to it

      Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

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

      HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How FOXN1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 17, with a bracket where FOXN1 sits. FOXN1 and 34 genes near it on chromosome 17, from 28,022,624 to 29,022,623.Chromosome 1717q11.2p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.328.2 Mb28.4 Mb28.6 Mb28.8 Mb29 MbNLK: 28,041,709–28,196,381, forward strandNLKTMEM97: 28,319,097–28,332,671, forward strandIFT20: 28,328,319–28,335,489, reverse strandTNFAIP1: 28,335,572–28,349,943, forward strandPOLDIP2: 28,343,133–28,357,623, reverse strandVMA12: 28,357,636–28,363,683, forward strandSEBOX: 28,363,506–28,365,199, reverse strand: 28,364,288–28,368,012, reverse strandSARM1: 28,364,356–28,404,049, forward strandSARM1VTN: 28,366,414–28,373,091, reverse strandVTNSLC46A1: 28,394,642–28,407,197, reverse strandSLC46A1RSKR: 28,455,752–28,614,210, reverse strandRSKRSLC13A2: 28,473,275–28,497,782, forward strandSLC13A2FOXN1: 28,506,348–28,538,900, forward strandFOXN1UNC119: 28,546,705–28,552,655, reverse strandUNC119PIGS: 28,553,383–28,571,794, reverse strandPIGSALDOC: 28,573,115–28,576,948, reverse strandALDOCSPAG5: 28,577,565–28,599,052, reverse strand: 28,580,012–28,614,185, reverse strandBLTP2: 28,614,440–28,645,454, reverse strandBLTP2SDF2: 28,648,346–28,662,189, reverse strandSDF2SUPT6H: 28,661,920–28,702,682, forward strandSUPT6HPROCA1: 28,703,196–28,712,313, reverse strandPROCA1RAB34: 28,713,545–28,719,594, reverse strandRAB34RPL23A: 28,719,940–28,724,365, forward strandRPL23ATLCD1: 28,723,435–28,727,935, reverse strandNEK8: 28,725,897–28,743,455, forward strandTRAF4: 28,743,978–28,772,894, forward strandFAM222B: 28,755,966–28,855,232, reverse strandFAM222BERAL1: 28,854,983–28,861,067, forward strandERAL1FLOT2: 28,879,335–28,897,741, reverse strandFLOT2DHRS13: 28,897,781–28,903,087, reverse strandDHRS13PHF12: 28,905,247–28,951,771, reverse strandPHF12PIPOX: 28,950,513–29,057,583, forward strandPIPOXSEZ6: 28,954,901–29,006,440, reverse strandSEZ6Diagram of FOXN1: 9 exons on the forward strand of chromosome 17Exon 2: 6 known disease-causing sitesExon 3: 6 known disease-causing sitesExon 4: 1 known disease-causing siteExon 5: 7 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 7: 12 known disease-causing sitesExon 8: 32 known disease-causing sitesExon 9: 1 known disease-causing siteExon 1: 28,506,348–28,506,443, 96 basesExon 2: 28,523,956–28,524,092, 137 basesExon 3: 28,524,503–28,524,967, 465 bases. 3 variants with a page in exon 3. List themExon 4: 28,527,251–28,527,361, 111 basesExon 5: 28,529,094–28,529,224, 131 bases. 2 variants with a page in exon 5. List themExon 6: 28,530,749–28,530,845, 97 bases. 3 variants with a page in exon 6. List themExon 7: 28,534,331–28,534,538, 208 bases. 6 variants with a page in exon 7. List themExon 8: 28,534,707–28,535,198, 492 bases. 15 variants with a page in exon 8. List themExon 9: 28,537,117–28,538,900, 1,784 bases1234567895′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 32.6 kb; 1,947 of those bases code for the protein.

How a genome test reads FOXN1

70

positions in FOXN1 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 32.6 kb of FOXN1, introns included, not only the 3.5 kb of exons.

Variants with a page (29)

The FOXN1 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
C82Xc.246C>AExon 328,524,625Pathogenic3 stars out of 4 reviewed by expert panel
D313Tfs*169c.933_936dupExon 728,534,334Pathogenic3 stars out of 4 reviewed by expert panel
E303Sfs*247c.907delExon 628,530,823Likely pathogenic3 stars out of 4 reviewed by expert panel
E390Kfs*160c.1168delExon 828,534,738Likely pathogenic3 stars out of 4 reviewed by expert panel
G337Efs*213c.1010delExon 728,534,411Likely pathogenic3 stars out of 4 reviewed by expert panel
H321Rc.962A>GExon 728,534,365Likely pathogenic3 stars out of 4 reviewed by expert panel
H457Pfs*93c.1370delExon 828,534,940Pathogenic3 stars out of 4 reviewed by expert panel
I433Ffs*117c.1296delExon 828,534,863Likely pathogenic3 stars out of 4 reviewed by expert panel
L325Pc.974T>CExon 728,534,377Likely pathogenic3 stars out of 4 reviewed by expert panel
L426Tfs*123c.1275_1278delExon 828,534,840Likely pathogenic3 stars out of 4 reviewed by expert panel

See all 29 FOXN1 variants →

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.). FOXN1 gene: forkhead box N1. Retrieved 16 October 2026, from https://dantelabs.com/genes/foxn1

Vancouver

Dante Labs. FOXN1 gene: forkhead box N1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/foxn1

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