GeneBe

F10

coagulation factor X, the group of Gla domain containing

Basic information

Region (hg38): 13:113122799-113149529

Links

ENSG00000126218 ∙ NCBI:2159 ∙ OMIM:613872 ∙ HGNC:3528 ∙ Uniprot:P00742 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • congenital factor X deficiency (Strong), mode of inheritance: AR
  • congenital factor X deficiency (Definitive), mode of inheritance: AR
  • congenital factor X deficiency (Supportive), mode of inheritance: AR
  • congenital factor X deficiency (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Factor X deficiencyARHematologic; PharmacogenomicIndividuals can suffer from bleeding diatheses of varying severity, and preventive measures related to bleeding episodes can be beneficial, including in special circumstances such as pregnancy; Precautions should be taken related to certain agents that may provoke/worsen bleeding riskHematologic5450692; 4989292; 4995085; 3732313; 8192155; 3408671; 2567188; 2790181; 1985698; 1997381; 9695984; 10746568; 12028042; 22151249; 22460599; 22506295

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the F10 gene.

  • Hereditary_factor_X_deficiency_disease (68 variants)
  • not_provided (33 variants)
  • Factor_X_deficiency (27 variants)
  • Inborn_genetic_diseases (26 variants)
  • F10-related_disorder (11 variants)
  • Abnormal_bleeding (5 variants)
  • Thrombocytopenia (3 variants)
  • not_specified (3 variants)
  • Factor_x_deficiency,_autosomal_dominant (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the F10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000504.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
7
clinvar
8
clinvar
1
clinvar
 17
missense
13
clinvar
20
clinvar
59
clinvar
3
clinvar
3
clinvar
 98
nonsense
2
clinvar
1
clinvar
 3
start loss
0
frameshift
3
clinvar
3
clinvar
 6
splice donor/acceptor (+/-2bp)
4
clinvar
 4
Total 18 29 66 11 4

Highest pathogenic variant AF is 0.000025310464

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
F10protein_codingprotein_codingENST00000375559 826716
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000002350.9131257150331257480.000131
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.202453040.8070.00002113218
Missense in Polyphen86133.730.643071399
Synonymous0.4611261330.9490.0000109912
Loss of Function1.671220.00.5999.42e-7235

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002440.000242
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0002370.000231
European (Non-Finnish)0.0001150.000114
Middle Eastern0.0001090.000109
South Asian0.0001960.000196
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
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.;
Disease
DISEASE: Factor X deficiency (FA10D) [MIM:227600]: A hemorrhagic disease with variable presentation. Affected individuals can manifest prolonged nasal and mucosal hemorrhage, menorrhagia, hematuria, and occasionally hemarthrosis. Some patients do not have clinical bleeding diathesis. {ECO:0000269|PubMed:10468877, ECO:0000269|PubMed:10739379, ECO:0000269|PubMed:10746568, ECO:0000269|PubMed:11248282, ECO:0000269|PubMed:11728527, ECO:0000269|PubMed:12574802, ECO:0000269|PubMed:12945883, ECO:0000269|PubMed:15075089, ECO:0000269|PubMed:15650540, ECO:0000269|PubMed:17393015, ECO:0000269|PubMed:19135706, ECO:0000269|PubMed:1973167, ECO:0000269|PubMed:1985698, ECO:0000269|PubMed:25313940, ECO:0000269|PubMed:26222694, ECO:0000269|PubMed:2790181, ECO:0000269|PubMed:7669671, ECO:0000269|PubMed:7860069, ECO:0000269|PubMed:8529633, ECO:0000269|PubMed:8845463, ECO:0000269|PubMed:8910490}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Complement and coagulation cascades - Homo sapiens (human);Warfarin Pathway, Pharmacodynamics;Aminocaproic Acid Action Pathway;Tranexamic Acid Action Pathway;Urokinase Action Pathway;Reteplase Action Pathway;Streptokinase Action Pathway;Tenecteplase Action Pathway;Alteplase Action Pathway;Anistreplase Action Pathway;Aprotinin Action Pathway;Phenindione Action Pathway;Dicoumarol Action Pathway;Warfarin Action Pathway;Acenocoumarol Action Pathway;Coagulation ;Bivalirudin Action Pathway;Argatroban Action Pathway;Ardeparin Action Pathway;Heparin Action Pathway;Fondaparinux Action Pathway;Enoxaparin Action Pathway;Phenprocoumon Action Pathway;Dicumarol Action Pathway;Ximelagatran Action Pathway;Lepirudin Action Pathway;Blood Clotting Cascade;Human Complement System;Dengue-2 Interactions with Complement and Coagulation Cascades;Dengue-2 Interactions with Blood Clotting Cascade;Complement and Coagulation Cascades;intrinsic prothrombin activation pathway;Post-translational protein modification;Metabolism of proteins;Gamma-carboxylation of protein precursors;Removal of aminoterminal propeptides from gamma-carboxylated proteins;Gamma-carboxylation, transport, and amino-terminal cleavage of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Extrinsic Pathway of Fibrin Clot Formation;Intrinsic Pathway of Fibrin Clot Formation;Hemostasis;Common Pathway of Fibrin Clot Formation;Formation of Fibrin Clot (Clotting Cascade);Beta2 integrin cell surface interactions;extrinsic prothrombin activation pathway (Consensus)

Recessive Scores

pRec
0.456

Intolerance Scores

loftool
0.107
rvis_EVS
-0.55
rvis_percentile_EVS
19.86

Haploinsufficiency Scores

pHI
0.144
hipred
Y
hipred_score
0.645
ghis
0.534

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.913

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
F10
Phenotype
cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name
f10
Affected structure
muscle
Phenotype tag
abnormal
Phenotype quality
hemorrhagic

Gene ontology

Biological process
proteolysis;endoplasmic reticulum to Golgi vesicle-mediated transport;blood coagulation;blood coagulation, extrinsic pathway;positive regulation of cell migration;positive regulation of protein kinase B signaling
Cellular component
extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;plasma membrane;intrinsic component of external side of plasma membrane
Molecular function
serine-type endopeptidase activity;calcium ion binding;protein binding;phospholipid binding