F10 (coagulation factor X)

Gene

• Entrez ID: 2159
• Gene name: Coagulation factor X
• Gene symbol: F10
• Synonyms (NCBI Gene): FX, FXA
• Chromosome: 13
• Chromosome location: 13q34
• Summary: This gene encodes the vitamin K-dependent coagulation factor X of the blood coagulation cascade. This factor undergoes multiple processing steps before its preproprotein is converted to a mature two-chain form by the excision of the tripeptide RKR. Two ch

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894392	C>G,T	Pathogenic	3 prime UTR variant, missense variant, coding sequence variant
rs121964948	A>T	Pathogenic	Intron variant, missense variant, coding sequence variant
rs368225671	G>A	Likely-pathogenic	Coding sequence variant, missense variant, intron variant
rs387906506	C>-	Pathogenic	Stop gained, coding sequence variant
rs1085307979	G>A	Likely-pathogenic	Coding sequence variant, 3 prime UTR variant, missense variant
rs1595098100	AACACCTGTCCACCTGGCCAGCCACACTGAGCCTGTCACGTCTGTCACAGGCCCTGCTCATCAATGAGGAAAACGAGGGTTTCTGTGGTGGAACCATTCTGAGCGAGTTCTACATCCTAACGGCAGCCCACTGTCTCTACCAAGCCAAGAGATTCAAGGTGAGGGTAGGTAAGTGACCAACAGCCCCCAGGGCCGTGGTGAGG>-	Likely-pathogenic	Splice acceptor variant, coding sequence variant, splice donor variant, intron variant
rs1595099527	G>A	Likely-pathogenic	Missense variant, 3 prime UTR variant, coding sequence variant
rs1595099645	T>C	Likely-pathogenic	Missense variant, 3 prime UTR variant, coding sequence variant
rs1595099844	G>A	Likely-pathogenic	Missense variant, 3 prime UTR variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016852	hsa-miR-335-5p	Microarray	18185580

Transcription factors

Transcription factor	Regulation	Reference
SP1	Unknown	8567696

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004252	Function	Serine-type endopeptidase activity	IBA
GO:0004252	Function	Serine-type endopeptidase activity	IDA	17469850
GO:0004252	Function	Serine-type endopeptidase activity	IEA
GO:0004252	Function	Serine-type endopeptidase activity	IMP	12574802
GO:0004252	Function	Serine-type endopeptidase activity	TAS	3011603
GO:0005509	Function	Calcium ion binding	IEA
GO:0005515	Function	Protein binding	IPI	6323392, 20427285, 32296183
GO:0005543	Function	Phospholipid binding	IDA	17469850
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	NAS	14718574
GO:0005576	Component	Extracellular region	TAS	3011603
GO:0005615	Component	Extracellular space	IBA
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005796	Component	Golgi lumen	IEA
GO:0005796	Component	Golgi lumen	TAS
GO:0005886	Component	Plasma membrane	TAS
GO:0006508	Process	Proteolysis	IBA
GO:0006508	Process	Proteolysis	IEA
GO:0007596	Process	Blood coagulation	IBA
GO:0007596	Process	Blood coagulation	IC	17469850
GO:0007596	Process	Blood coagulation	IEA
GO:0007596	Process	Blood coagulation	TAS	6587384
GO:0007599	Process	Hemostasis	IEA
GO:0008233	Function	Peptidase activity	IEA
GO:0008236	Function	Serine-type peptidase activity	IEA
GO:0009897	Component	External side of plasma membrane	IC	17469850
GO:0016787	Function	Hydrolase activity	IEA
GO:0030335	Process	Positive regulation of cell migration	TAS	18612547
GO:0032008	Process	Positive regulation of TOR signaling	IDA	18612547
GO:0032008	Process	Positive regulation of TOR signaling	IEA

Other IDs

• MIM: 613872
• HGNC: 3528
• e!Ensembl: ENSG00000126218

Protein

• UniProt ID: P00742
• Protein name: Coagulation factor X (EC 3.4.21.6) (Stuart factor) (Stuart-Prower factor) [Cleaved into: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain]
• Protein function: Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting (PubMed:22409427). Factor Xa activates pro-inflammatory signaling pathways in a pr
• PDB: 1C5M, 1EZQ, 1F0R, 1F0S, 1FAX, 1FJS, 1FXY, 1G2L, 1G2M, 1HCG, 1IOE, 1IQE, 1IQF, 1IQG, 1IQH, 1IQI, 1IQJ, 1IQK, 1IQL, 1IQM, 1IQN, 1KSN, 1LPG, 1LPK, 1LPZ, 1LQD, 1MQ5, 1MQ6, 1NFU, 1NFW, 1NFX, 1NFY, 1P0S, 1V3X, 1WU1, 1XKA, 1XKB, 1Z6E, 2BMG, 2BOH, 2BOK, 2BQ6, 2BQ7, 2BQW, 2CJI, 2D1J, 2EI6, 2EI7, 2EI8, 2FZZ, 2G00
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00594	Gla	45 → 85	Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain	Domain
  PF00008	EGF	90 → 120	EGF-like domain	Domain
  PF14670	FXa_inhibition	129 → 164		Domain
  PF00089	Trypsin	235 → 462	Trypsin	Domain

• Tissue specificity: TISSUE SPECIFICITY: Plasma; synthesized in the liver. {ECO:0000269|PubMed:6587384}.
• Sequence:

  MGRPLHLVLLSASLAGLLLLGESLFIRREQANNILARVTRANSFLEEMKKGHLERECMEE
  TCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGKCKDGLGEYTCTCLEGFEGKN
  CELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERR
  KRSVAQATSSSGEAPDSITWKPYDAADLDPTENPFDLLDFNQTQPERGDNNLTRIVGGQE
  CKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGE
  AVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGI
  VSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSG
  GPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKAKSHAPE
  VITSSPLK

• Sequence length: 488

Pathways

KEGG:

Complement and coagulation cascades

Reactome:

Extrinsic Pathway of Fibrin Clot Formation
Intrinsic Pathway of Fibrin Clot Formation
Common 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

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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Abnormal bleeding	Likely pathogenic	rs1595098100	RCV000852256	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
F10-related disorder	Likely pathogenic	rs768222784, rs121964944	RCV004731246 RCV003983201	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Factor X deficiency	Pathogenic; Likely pathogenic	rs2138548669, rs768222784, rs104894392, rs387906506, rs121964947, rs121964940, rs753790195, rs121964948, rs121964941, rs121964942, rs121964943, rs121964945, rs121964944	RCV001420416 RCV002267785 RCV000012833 RCV000012834 RCV000012836 RCV000012837 RCV000012838 RCV000012839 RCV000012840 RCV000012842 RCV000012843 RCV000012845 RCV001824369	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Factor x deficiency, autosomal dominant	Pathogenic	rs121964946	RCV000012846	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary factor X deficiency disease	Pathogenic; Likely pathogenic	rs376163818, rs369872236, rs768222784, rs1325135019, rs749213415, rs2138557799, rs1250509122, rs2503095549, rs2503094343, rs2503081595, rs2503094311, rs2503095616, rs2503095628, rs2503081410, rs755110383, rs773214680, rs2036592550, rs121964944, rs1595099527, rs1595099645, rs1595099844	RCV001834560 RCV002222132 RCV002236395 RCV002245313 RCV002245314 RCV002245315 RCV002245496 RCV003445226 RCV003445227 RCV003445228 RCV003445229 RCV003445230 RCV003445231 RCV003313859 RCV003313867 RCV003313881 RCV003990425 RCV000852044 RCV000851652 RCV000851584 RCV000851588	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BLOOD COAGULATION DISORDERS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL FACTOR X DEFICIENCY	—	ClinGen, GenCC, Orphanet ClinGen, GenCC, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DENTAL CARIES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PREECLAMPSIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIATIC ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thrombocytopenia	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
THROMBOSIS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VENOUS THROMBOEMBOLISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations