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Gene

FOXJ1

forkhead box J1

Summary

Cytogenetic location
17q25.1
Coordinates
Chromosome 17: 76,136,333–76,141,245 (GRCh38)
Exons
3 exons across 4.9 kb
Protein
421 amino acids
Inheritance
Autosomal recessive
Also known as
HFH-4, HFH4
Previous symbols
FKHL13
MANE Select transcript
ENST00000322957.7NM_001454.4
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 report relevant to this gene

  • Primary Ciliary Dyskinesia

    • Autosomal recessive

      A rare, genetically heterogeneous, primarily respiratory disorder characterized by chronic upper and lower respiratory tract disease. Approximately half of PCD patients have an organ laterality defect (situs inversus totalis or situs ambiguus/heterotaxy).

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

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 FOXJ1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 17, with a bracket where FOXJ1 sits. FOXJ1 and 37 genes near it on chromosome 17, from 75,638,789 to 76,638,788.Chromosome 1717q25.1p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.375.8 Mb76 Mb76.2 Mb76.4 Mb76.6 MbRECQL5: 75,626,839–75,667,197, reverse strandRECQL5SMIM5: 75,628,368–75,642,570, forward strandSMIM5ERLN: 75,646,243–75,647,975, forward strandERLNSAP30BP: 75,667,230–75,708,062, forward strandSAP30BPITGB4: 75,721,190–75,757,821, forward strandITGB4GALK1: 75,751,470–75,765,251, reverse strandGALK1H3-3B: 75,776,434–75,785,893, reverse strandH3-3BUNK: 75,784,799–75,825,799, forward strandUNKUNC13D: 75,827,032–75,845,353, reverse strandUNC13DWBP2: 75,845,699–75,856,507, reverse strandWBP2TRIM47: 75,874,161–75,878,637, reverse strandTRIM65: 75,879,538–75,897,018, reverse strandTRIM65MRPL38: 75,898,642–75,905,097, reverse strandMRPL38: 75,898,645–75,930,129, reverse strandFBF1: 75,908,212–75,941,140, reverse strandFBF1ACOX1: 75,941,507–75,979,459, reverse strandACOX1TEN1: 75,979,212–76,000,587, forward strandTEN1TEN1-CDK3: 75,979,231–76,005,999, forward strandTEN1-CDK3CDK3: 76,000,644–76,005,999, forward strandCDK3EVPL: 76,004,379–76,027,465, reverse strandEVPLSRP68: 76,037,989–76,072,718, reverse strandSRP68ZACN: 76,071,961–76,083,666, forward strandZACNGALR2: 76,074,773–76,077,537, forward strandGALR2EXOC7: 76,080,995–76,121,576, reverse strandEXOC7FOXJ1: 76,136,333–76,141,245, reverse strandFOXJ1RNF157: 76,142,460–76,240,662, reverse strandRNF157UBALD2: 76,265,197–76,271,298, forward strandUBALD2QRICH2: 76,274,049–76,308,282, reverse strandQRICH2PRPSAP1: 76,309,478–76,384,521, reverse strandPRPSAP1SPHK1: 76,376,584–76,387,860, forward strandSPHK1UBE2O: 76,389,456–76,453,226, reverse strandUBE2OAANAT: 76,452,749–76,470,122, forward strandAANATRHBDF2: 76,470,884–76,501,790, reverse strandRHBDF2CYGB: 76,527,356–76,551,175, reverse strandCYGBPRCD: 76,527,586–76,553,578, forward strandPRCD: 76,563,710–76,569,724, reverse strandST6GALNAC2: 76,564,424–76,586,956, reverse strandST6GALNAC2ST6GALNAC1: 76,624,228–76,643,907, reverse strandST6GALNAC1Diagram of FOXJ1: 3 exons on the reverse strand of chromosome 17Exon 3: 3 known disease-causing sitesExon 3: 76,136,333–76,138,120, 1,788 basesExon 2: 76,139,898–76,140,564, 667 basesExon 1: 76,141,114–76,141,245, 132 bases3215′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 2.6 kb of the gene's 4.9 kb; 1,266 of those bases code for the protein.

How a genome test reads FOXJ1

3

positions in FOXJ1 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 4.9 kb of FOXJ1, introns included, not only the 2.6 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.). FOXJ1 gene: forkhead box J1. Retrieved 16 October 2026, from https://dantelabs.com/genes/foxj1

Vancouver

Dante Labs. FOXJ1 gene: forkhead box J1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/foxj1

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