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F9 coagulation factor IX [ Homo sapiens (human) ]

Gene ID: 2158, updated on 14-Apr-2016
Official Symbol
F9provided by HGNC
Official Full Name
coagulation factor IXprovided by HGNC
Primary source
HGNC:HGNC:3551
See related
Ensembl:ENSG00000101981 HPRD:02385; MIM:300746; Vega:OTTHUMG00000022536
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FIX; P19; PTC; HEMB; THPH8; F9 p22
Summary
This gene encodes vitamin K-dependent coagulation factor IX that circulates in the blood as an inactive zymogen. This factor is converted to an active form by factor XIa, which excises the activation peptide and thus generates a heavy chain and a light chain held together by one or more disulfide bonds. The role of this activated factor IX in the blood coagulation cascade is to activate factor X to its active form through interactions with Ca+2 ions, membrane phospholipids, and factor VIII. Alterations of this gene, including point mutations, insertions and deletions, cause factor IX deficiency, which is a recessive X-linked disorder, also called hemophilia B or Christmas disease. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Sep 2015]
Orthologs
Location:
Xq27.1-q27.2
Exon count:
8
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) X NC_000023.11 (139530734..139563464)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (138612889..138645617)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SNRPN upstream reading frame-like (pseudogene) Neighboring gene steroid 5 alpha-reductase 1 pseudogene 1 Neighboring gene MCF.2 cell line derived transforming sequence Neighboring gene brain cytoplasmic RNA 1, pseudogene 1

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Hereditary factor IX deficiency disease
MedGen: C0008533 OMIM: 306900 GeneReviews: Hemophilia B
Compare labs
Thrombophilia, X-linked, due to factor IX defect
MedGen: C2749016 OMIM: 300807 GeneReviews: Not available
Compare labs
Warfarin response
MedGen: CN078029 OMIM: 122700 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

ClinGen Genome Curation Page
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC129641, MGC129642

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
endopeptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
serine-type endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
ER to Golgi vesicle-mediated transport TAS
Traceable Author Statement
more info
 
blood coagulation IDA
Inferred from Direct Assay
more info
PubMed 
blood coagulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
blood coagulation, extrinsic pathway TAS
Traceable Author Statement
more info
 
blood coagulation, intrinsic pathway TAS
Traceable Author Statement
more info
 
peptidyl-glutamic acid carboxylation TAS
Traceable Author Statement
more info
 
proteolysis IDA
Inferred from Direct Assay
more info
PubMed 
signal peptide processing TAS
Traceable Author Statement
more info
 
zymogen activation IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi lumen TAS
Traceable Author Statement
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region NAS
Non-traceable Author Statement
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
Preferred Names
coagulation factor IX
Names
Christmas factor
factor 9
factor IX F9
plasma thromboplastic component
plasma thromboplastin component
NP_000124.1

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007994.1 RefSeqGene

    Range
    5001..37723
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_556

mRNA and Protein(s)

  1. NM_000133.3NP_000124.1  coagulation factor IX isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_000124.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL033403, BC109214, M11309
    Consensus CDS
    CCDS14666.1
    UniProtKB/Swiss-Prot
    P00740
    Related
    ENSP00000218099, OTTHUMP00000024154, ENST00000218099, OTTHUMT00000058557
    Conserved Domains (5) summary
    smart00020
    Location:226454
    Tryp_SPc; Trypsin-like serine protease
    smart00069
    Location:2892
    GLA; Domain containing Gla (gamma-carboxyglutamate) residues
    cd00054
    Location:93129
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00190
    Location:227457
    Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...
    pfam14670
    Location:134170
    FXa_inhibition; Coagulation Factor Xa inhibitory site
  2. NM_001313913.1NP_001300842.1  coagulation factor IX isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform 1.
    Source sequence(s)
    AB186358, AL033403, BC109214, M11309
    UniProtKB/Swiss-Prot
    P00740
    Conserved Domains (4) summary
    smart00020
    Location:188416
    Tryp_SPc; Trypsin-like serine protease
    smart00069
    Location:2892
    GLA; Domain containing Gla (gamma-carboxyglutamate) residues
    cd00190
    Location:189419
    Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...
    pfam14670
    Location:96132
    FXa_inhibition; Coagulation Factor Xa inhibitory site

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p2 Primary Assembly

    Range
    139530734..139563464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005262397.3XP_005262454.1  

    Conserved Domains (4) summary
    smart00020
    Location:183411
    Tryp_SPc; Trypsin-like serine protease
    smart00069
    Location:2892
    GLA; Domain containing Gla (gamma-carboxyglutamate) residues
    cd00054
    Location:93129
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00190
    Location:184414
    Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 Alternate CHM1_1.1

    Range
    138523783..138556510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)