Gene Gene information from NCBI Gene database.
Entrez ID 2158
Gene name Coagulation factor IX
Gene symbol F9
Synonyms (NCBI Gene)
F9 p22FIXHEMBP19PTCTHPH8
Chromosome X
Chromosome location Xq27.1
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 ch
SNPs SNP information provided by dbSNP.
137
SNP ID Visualize variation Clinical significance Consequence
rs1801202 C>T Benign, conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant
rs137852223 C>G,T Pathogenic Coding sequence variant, stop gained, missense variant
rs137852224 T>C Likely-pathogenic Coding sequence variant, missense variant
rs137852226 A>T Pathogenic Coding sequence variant, missense variant
rs137852227 C>T Pathogenic Coding sequence variant, stop gained
miRNA miRNA information provided by mirtarbase database.
98
miRTarBase ID miRNA Experiments Reference
MIRT715255 hsa-miR-6845-3p HITS-CLIP 19536157
MIRT715254 hsa-miR-302b-5p HITS-CLIP 19536157
MIRT715253 hsa-miR-302d-5p HITS-CLIP 19536157
MIRT715252 hsa-miR-7106-3p HITS-CLIP 19536157
MIRT715255 hsa-miR-6845-3p HITS-CLIP 19536157
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
CEBPA Activation 8075306
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
37
GO ID Ontology Definition Evidence Reference
GO:0004175 Function Endopeptidase activity IDA 2592373, 20121197
GO:0004175 Function Endopeptidase activity IEA
GO:0004252 Function Serine-type endopeptidase activity IBA
GO:0004252 Function Serine-type endopeptidase activity IEA
GO:0004252 Function Serine-type endopeptidase activity NAS 8632006
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300746 3551 ENSG00000101981
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P00740
Protein name Coagulation factor IX (EC 3.4.21.22) (Christmas factor) (Plasma thromboplastin component) (PTC) [Cleaved into: Coagulation factor IXa light chain; Coagulation factor IXa heavy chain]
Protein function Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa. {ECO:0000269|PubMed:1730
PDB 1CFH , 1CFI , 1EDM , 1IXA , 1MGX , 1NL0 , 1RFN , 2WPH , 2WPI , 2WPJ , 2WPK , 2WPL , 2WPM , 3KCG , 3LC3 , 3LC5 , 4WM0 , 4WMA , 4WMB , 4WMI , 4WMK , 4WN2 , 4WNH , 4YZU , 4Z0K , 4ZAE , 5EGM , 5F84 , 5F85 , 5F86 , 5JB8 , 5JB9 , 5JBA , 5JBB , 5JBC , 5TNO , 5TNT , 5VYG , 6MV4 , 6RFK , 6X5J , 6X5L , 6X5P , 7AHV , 8EPC , 8EPH , 8EPK , 8OL9 , 9BVK , 9BVR
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00594 Gla 52 92 Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain Domain
PF00008 EGF 97 127 EGF-like domain Domain
PF14670 FXa_inhibition 134 170 Domain
PF00089 Trypsin 227 454 Trypsin Domain
Tissue specificity TISSUE SPECIFICITY: Detected in blood plasma (at protein level) (PubMed:19846852, PubMed:2592373, PubMed:3857619, PubMed:8295821, PubMed:9169594). Synthesized primarily in the liver and secreted in plasma. {ECO:0000269|PubMed:19846852, ECO:0000269|PubMed:
Sequence
Sequence length 461
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Complement and coagulation cascades   Extrinsic Pathway of Fibrin Clot Formation
Intrinsic Pathway of Fibrin Clot Formation
Gamma-carboxylation of protein precursors
Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus
Removal of aminoterminal propeptides from gamma-carboxylated proteins
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
26
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of coagulation Pathogenic rs137852247, rs1603264300 RCV000851897
RCV000851757
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
F9-related disorder Pathogenic; Likely pathogenic rs137852233, rs137852240, rs137852241, rs137852254, rs137852255, rs137852261, rs1287011273, rs1330705989, rs2520803292, rs1371750567, rs1224128266, rs1927766998, rs1275708479 RCV003430636
RCV003407315
RCV004752695
RCV004752696
RCV004730842
View all (8 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
HEMOPHILIA B BRANDENBURG Pathogenic rs2148352851 RCV000011399
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hemophilia B leyden Pathogenic; Likely pathogenic rs1178811105, rs2148352878, rs2148352869, rs1927322453, rs1927322926, rs1166164399 RCV000011304
RCV000011307
RCV000011390
RCV000011391
RCV000011392
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
BIPOLAR DISORDER Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BLEEDING DISORDER IN HEMOPHILIA B CARRIERS Disgenet, Orphanet
Disgenet, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Deep venous thrombosis, protection against Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
F9 POLYMORPHISM Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Activated Protein C Resistance Activated Protein C Resistance BEFREE 23015030
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia BEFREE 21681782
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 8946928
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 3042790, 30914194
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of pancreas Pancreatic adenocarcinoma BEFREE 28261999
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma, Oxyphilic Adenocarcinoma BEFREE 24559275, 28816539
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma, Tubular Adenocarcinoma BEFREE 30349383
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 10646882, 15126554, 17639054
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 24702198, 27623068, 28314770, 9841749
★☆☆☆☆
Found in Text Mining only
Adult T-Cell Lymphoma/Leukemia T-Cell Lymphoma/Leukemia BEFREE 2787798, 3872164, 6090008, 6331549, 6833950, 8946928
★☆☆☆☆
Found in Text Mining only