F9 coagulation factor IX [Homo sapiens (human)] - Gene

Summary

Official Symbol: F9provided by HGNC
Official Full Name: coagulation factor IXprovided by HGNC
Primary source: HGNC:HGNC:3551
See related: Ensembl:ENSG00000101981 MIM:300746; AllianceGenome:HGNC:3551
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]
Expression: Restricted expression toward liver (RPKM 181.1) See more
Orthologs: mouse all
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Genomic context

Location:: Xq27.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (139530739..139563459)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (137842731..137875455)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (138612898..138645618)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study on the Mutation of F Gene in 31 Patients with Type B Hemophilia.
Title: Study on the Mutation of FⅨ Gene in 31 Patients with Type B Hemophilia.
Crippling down factor IX for therapeutic gain.
Title: Crippling down factor IX for therapeutic gain.
Factor IXa variants resistant to plasma inhibitors enhance clot formation in vivo.
Title: Factor IXa variants resistant to plasma inhibitors enhance clot formation in vivo.
Whole F9 gene sequencing identified deep intronic variations in genetically unresolved hemophilia B patients.
Title: Whole F9 gene sequencing identified deep intronic variations in genetically unresolved hemophilia B patients.
Structural and functional exploration of three newly identified coagulation factor IX mutations in Chinese hemophilia B patients.
Title: Structural and functional exploration of three newly identified coagulation factor IX mutations in Chinese hemophilia B patients.
An updated interactive database for 1692 genetic variants in coagulation factor IX provides detailed insights into hemophilia B.
Title: An updated interactive database for 1692 genetic variants in coagulation factor IX provides detailed insights into hemophilia B.
Liver-heart cross-talk mediated by coagulation factor XI protects against heart failure.
Title: Liver-heart cross-talk mediated by coagulation factor XI protects against heart failure.
Platelet Activation via Glycoprotein VI Initiates Thrombin Generation: A Potential Role for Platelet-Derived Factor IX?
Title: Platelet Activation via Glycoprotein VI Initiates Thrombin Generation: A Potential Role for Platelet-Derived Factor IX?
[Analysis of hereditary coagulation factor deficiency in a Chinese pedigree with compound heterozygous mutations].
Title: [Analysis of hereditary coagulation factor Ⅺ deficiency in a Chinese pedigree with compound heterozygous mutations].
Effects of 14 F9 synonymous codon variants on hemophilia B expression: Alteration of splicing along with protein expression.
Title: Effects of 14 F9 synonymous codon variants on hemophilia B expression: Alteration of splicing along with protein expression.

Submit: New GeneRIF Correction See all GeneRIFs (192)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Hereditary factor IX deficiency disease MedGen: C0008533 OMIM: 306900 GeneReviews: Hemophilia B	not available
Thrombophilia, X-linked, due to factor 9 defect MedGen: C2749016 OMIM: 300807 GeneReviews: Not available	not available
Warfarin sensitivity, X-linked MedGen: C5393318 OMIM: 301052 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2021-01-12) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-12) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:197038 (e-PCR)
- UniSTS:155919

GDB:197039 (e-PCR)
- UniSTS:155920

G28615 (e-PCR)
- UniSTS:56096

GDB:177588 (e-PCR)
- UniSTS:154932

GDB:177796 (e-PCR)
- UniSTS:154962

F9 (e-PCR), detects polymorphism
- UniSTS:525911

GDB:177926 (e-PCR)
- UniSTS:154982

RH17659 (e-PCR)
- UniSTS:22655

GDB:178640 (e-PCR)
- UniSTS:155035

G66627 (e-PCR)
- UniSTS:166822

G66628 (e-PCR)
- UniSTS:166823

G66629 (e-PCR)
- UniSTS:166824

F9 (e-PCR), detects polymorphism
- UniSTS:266922

GDB:181635 (e-PCR)
- UniSTS:155321

GDB:181846 (e-PCR)
- UniSTS:155334

GDB:182120 (e-PCR)
- UniSTS:155347

GDB:182121 (e-PCR)
- UniSTS:155348

GDB:182122 (e-PCR)
- UniSTS:155349

F9_627 (e-PCR)
- UniSTS:277225

F9_V31 (e-PCR)
- UniSTS:277225

G10618 (e-PCR)
- UniSTS:21481

GDB:303850 (e-PCR)
- UniSTS:156398

GDB:192503 (e-PCR)
- UniSTS:99325

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	EXP Inferred from Experiment more info	PubMed
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables endopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	EXP Inferred from Experiment more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables serine-type endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables serine-type endopeptidase activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in blood coagulation	IBA Inferred from Biological aspect of Ancestor more info
involved_in blood coagulation	IDA Inferred from Direct Assay more info	PubMed
involved_in blood coagulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteolysis	IDA Inferred from Direct Assay more info	PubMed
involved_in zymogen activation	IBA Inferred from Biological aspect of Ancestor more info
involved_in zymogen activation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: coagulation factor IX

Names: Christmas factor; factor 9; factor IX F9; plasma thromboplastic component; plasma thromboplastin component

NP_000124.1

EC 3.4.21.22

NP_001300842.1

EC 3.4.21.22

XP_005262454.1

EC 3.4.21.22

XP_054182657.1

EC 3.4.21.22

NCBI Reference Sequences (RefSeq)

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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

NG_007994.1 RefSeqGene

Range

5001..37723

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_556

mRNA and Protein(s)

NM_000133.4 → NP_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

A8K9N4, F2RM36, P00740, Q5FBE1, Q5JYJ8

UniProtKB/TrEMBL

F2RM37

Related

ENSP00000218099.2, ENST00000218099.7

Conserved Domains (4) summary

smart00069
Location:28 → 92

GLA; Domain containing Gla (gamma-carboxyglutamate) residues

cd00054
Location:93 → 129

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:227 → 457

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:134 → 170

FXa_inhibition; Coagulation Factor Xa inhibitory site
NM_001313913.2 → NP_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

Consensus CDS

CCDS83495.1

UniProtKB/TrEMBL

F2RM37

Related

ENSP00000377650.2, ENST00000394090.2

Conserved Domains (4) summary

smart00020
Location:188 → 416

Tryp_SPc; Trypsin-like serine protease

smart00069
Location:28 → 92

GLA; Domain containing Gla (gamma-carboxyglutamate) residues

cd00190
Location:189 → 419

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:96 → 132

FXa_inhibition; Coagulation Factor Xa inhibitory site

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

139530739..139563459

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005262397.5 → XP_005262454.1 coagulation factor IX isoform X1

UniProtKB/TrEMBL

F2RM37

Conserved Domains (4) summary

smart00020
Location:183 → 411

Tryp_SPc; Trypsin-like serine protease

smart00069
Location:28 → 92

GLA; Domain containing Gla (gamma-carboxyglutamate) residues

cd00054
Location:93 → 129

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:184 → 414

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 ...