F3
coagulation factor III, tissue factor, the group of CD molecules
Basic information
Region (hg38): 1:94529173-94541759
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the F3 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 11 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 4 | 4 |
Variants in F3
This is a list of pathogenic ClinVar variants found in the F3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-94530477-G-A | not specified | Uncertain significance (Feb 06, 2023) | ||
| 1-94530506-C-T | Benign (Jul 18, 2018) | |||
| 1-94530534-T-C | not specified | Likely benign (Nov 09, 2021) | ||
| 1-94530555-T-C | not specified | Uncertain significance (Dec 20, 2021) | ||
| 1-94530582-T-C | not specified | Likely benign (Mar 19, 2024) | ||
| 1-94530594-T-G | not specified | Uncertain significance (Jun 11, 2024) | ||
| 1-94532377-C-T | not specified | Likely benign (Apr 09, 2024) | ||
| 1-94533095-C-T | not specified | Uncertain significance (Mar 29, 2022) | ||
| 1-94533155-G-A | not specified | Uncertain significance (Aug 09, 2021) | ||
| 1-94533159-G-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 1-94533166-A-G | Uncertain significance (Nov 01, 2022) | |||
| 1-94533175-T-C | not specified | Uncertain significance (Feb 06, 2024) | ||
| 1-94533194-G-A | Benign (Dec 31, 2019) | |||
| 1-94536012-C-T | not specified | Likely benign (Jan 02, 2024) | ||
| 1-94536026-GCT-G | Uncertain significance (Feb 09, 2022) | |||
| 1-94536072-G-A | not specified | Uncertain significance (Dec 11, 2023) | ||
| 1-94536099-T-C | Benign (Jul 06, 2018) | |||
| 1-94540309-T-C | Likely benign (May 19, 2018) | |||
| 1-94540351-C-T | Likely benign (Jul 02, 2018) | |||
| 1-94540363-T-C | Benign (Jun 06, 2018) | |||
| 1-94541549-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 1-94541588-C-T | not specified | Uncertain significance (Oct 14, 2023) | ||
| 1-94541615-G-A | not specified | Uncertain significance (Oct 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| F3 | protein_coding | protein_coding | ENST00000334047 | 6 | 12576 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0189 | 0.963 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.614 | 134 | 156 | 0.861 | 0.00000808 | 1901 |
| Missense in Polyphen | 40 | 52.569 | 0.7609 | 662 | ||
| Synonymous | 0.446 | 56 | 60.4 | 0.927 | 0.00000335 | 583 |
| Loss of Function | 2.07 | 5 | 13.1 | 0.382 | 6.36e-7 | 163 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000907 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000667 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Initiates blood coagulation by forming a complex with circulating factor VII or VIIa. The [TF:VIIa] complex activates factors IX or X by specific limited protolysis. TF plays a role in normal hemostasis by initiating the cell-surface assembly and propagation of the coagulation protease cascade. {ECO:0000269|PubMed:12652293}.;
- Pathway
- Complement and coagulation cascades - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);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;VEGFA-VEGFR2 Signaling Pathway;Dengue-2 Interactions with Complement and Coagulation Cascades;Macrophage markers;Macrophage markers;Complement and Coagulation Cascades;Extrinsic Pathway of Fibrin Clot Formation;Hemostasis;Formation of Fibrin Clot (Clotting Cascade);extrinsic prothrombin activation pathway
(Consensus)
Recessive Scores
- pRec
- 0.948
Intolerance Scores
- loftool
- 0.484
- rvis_EVS
- 0.88
- rvis_percentile_EVS
- 89.02
Haploinsufficiency Scores
- pHI
- 0.285
- hipred
- N
- hipred_score
- 0.338
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.848
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- F3
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; hematopoietic system 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); normal phenotype; 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); neoplasm; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- f3b
- Affected structure
- vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- hemorrhagic
Gene ontology
- Biological process
- positive regulation of endothelial cell proliferation;activation of plasma proteins involved in acute inflammatory response;activation of blood coagulation via clotting cascade;activation of cysteine-type endopeptidase activity involved in apoptotic process;blood coagulation;blood coagulation, extrinsic pathway;positive regulation of platelet-derived growth factor receptor signaling pathway;protein processing;cytokine-mediated signaling pathway;positive regulation of cell migration;positive regulation of angiogenesis;positive regulation of positive chemotaxis;positive regulation of protein kinase B signaling
- Cellular component
- extracellular space;plasma membrane;cell surface;integral component of membrane;intrinsic component of external side of plasma membrane;collagen-containing extracellular matrix;serine-type peptidase complex
- Molecular function
- protease binding;serine-type endopeptidase activity;cytokine receptor activity;protein binding;phospholipid binding