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Gene

F9

coagulation factor IX

Summary

Cytogenetic location
Xq27.1
Coordinates
Chromosome X: 139,530,739–139,563,459 (GRCh38)
Exons
8 exons across 32.7 kb
Protein
461 amino acids
Inheritance
X-linked recessive
Also known as
FIX
MANE Select transcript
ENST00000218099.7NM_000133.4
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

  • Haemophilia

    • HemophiliaX-linked recessive

      A group of bleeding disorders caused by deficiency of coagulation factor VIII (haemophilia A) or factor IX (haemophilia B).

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

      Factor replacement therapy, extended half-life factor products, emicizumab (bispecific antibody), immune tolerance therapy

  • Thrombophilia

    • Inherited Thrombophilia
      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Anticoagulation (duration by genotype); avoid estrogen-containing contraceptives; LMWH for pregnancy prophylaxis; extended post-surgical anticoagulation; lifelong anticoagulation for compound/high-risk genotypes

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 F9 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 X, with a bracket where F9 sits. F9 and 4 genes near it on chromosome X, from 139,047,099 to 140,047,098.Chromosome XXq27.1p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q28139.2 Mb139.4 Mb139.6 Mb139.8 Mb140 MbFGF13: 138,614,727–139,222,777, reverse strandFGF13F9: 139,530,739–139,563,459, forward strandF9MCF2: 139,581,770–139,708,216, reverse strandMCF2ATP11C: 139,726,289–139,945,276, reverse strandATP11CCXorf66: 139,955,728–139,965,525, reverse strandCXorf66Diagram of F9: 8 exons on the forward strand of chromosome XExon 1: 8 known disease-causing sitesExon 2: 21 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 4: 14 known disease-causing sitesExon 5: 16 known disease-causing sitesExon 6: 16 known disease-causing sitesExon 7: 16 known disease-causing sitesExon 8: 78 known disease-causing sitesExon 1: 139,530,739–139,530,852, 114 bases. 3 variants with a page in exon 1. List themExon 2: 139,537,010–139,537,173, 164 bases. 8 variants with a page in exon 2. List themExon 3: 139,537,362–139,537,386, 25 bases. 1 variant with a page in exon 3. List themExon 4: 139,541,076–139,541,189, 114 bases. 1 variant with a page in exon 4. List themExon 5: 139,548,363–139,548,491, 129 bases. 2 variants with a page in exon 5. List themExon 6: 139,551,062–139,551,264, 203 bases. 2 variants with a page in exon 6. List themExon 7: 139,560,741–139,560,855, 115 bases. 5 variants with a page in exon 7. List themExon 8: 139,561,524–139,563,459, 1,936 bases. 19 variants with a page in exon 8. List them124685′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 2.8 kb of the gene's 32.7 kb; 1,386 of those bases code for the protein.

How a genome test reads F9

186

positions in F9 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 32.7 kb of F9, introns included, not only the 2.8 kb of exons.

Variants with a page (44)

The F9 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
A279Tc.835G>AExon 7139,560,852Pathogenic3 stars out of 4 reviewed by expert panel
A337Pc.1009G>CExon 8139,561,694Likely pathogenic3 stars out of 4 reviewed by expert panel
A337Tc.1009G>AExon 8139,561,694Pathogenic3 stars out of 4 reviewed by expert panel
A337Vc.1010C>TExon 8139,561,695Pathogenic3 stars out of 4 reviewed by expert panel
c.88+1G>AIntron 1139,530,853Pathogenic3 stars out of 4 reviewed by expert panel
c.88+5G>TIntron 1139,530,857Likely pathogenic3 stars out of 4 reviewed by expert panel
c.138G>TExon 2139,537,059Pathogenic3 stars out of 4 reviewed by expert panel
c.520+13A>GIntron 5139,548,504Pathogenic3 stars out of 4 reviewed by expert panel
C268Gc.802T>GExon 7139,560,819Likely pathogenic3 stars out of 4 reviewed by expert panel
C268Rc.802T>CExon 7139,560,819Likely pathogenic3 stars out of 4 reviewed by expert panel

See all 44 F9 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.). F9 gene: coagulation factor IX. Retrieved 16 October 2026, from https://dantelabs.com/genes/f9

Vancouver

Dante Labs. F9 gene: coagulation factor IX [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/f9

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