FGF1
fibroblast growth factor 1, the group of Receptor ligands|Fibroblast growth factor family
Basic information
Region (hg38): 5:142592177-142698070
Previous symbols: [ "FGFA" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (6 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGF1 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 1 |
Variants in FGF1
This is a list of pathogenic ClinVar variants found in the FGF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-142595357-C-G | not specified | Uncertain significance (Jul 14, 2021) | ||
| 5-142595364-A-C | not specified | Uncertain significance (Jun 24, 2022) | ||
| 5-142595414-T-G | not specified | Uncertain significance (Aug 23, 2021) | ||
| 5-142600707-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 5-142600757-C-T | not specified | Uncertain significance (Mar 23, 2023) | ||
| 5-142614066-C-T | Benign (Dec 31, 2019) | |||
| 5-142614088-C-G | not specified | Uncertain significance (Jun 29, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FGF1 | protein_coding | protein_coding | ENST00000359370 | 3 | 105875 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.444 | 0.530 | 125740 | 1 | 3 | 125744 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.464 | 77 | 89.4 | 0.862 | 0.00000484 | 1022 |
| Missense in Polyphen | 32 | 38.952 | 0.82153 | 433 | ||
| Synonymous | -0.682 | 45 | 39.5 | 1.14 | 0.00000249 | 295 |
| Loss of Function | 1.78 | 1 | 5.49 | 0.182 | 2.29e-7 | 75 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000185 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00000888 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays an important role in the regulation of cell survival, cell division, angiogenesis, cell differentiation and cell migration. Functions as potent mitogen in vitro. Acts as a ligand for FGFR1 and integrins. Binds to FGFR1 in the presence of heparin leading to FGFR1 dimerization and activation via sequential autophosphorylation on tyrosine residues which act as docking sites for interacting proteins, leading to the activation of several signaling cascades. Binds to integrin ITGAV:ITGB3. Its binding to integrin, subsequent ternary complex formation with integrin and FGFR1, and the recruitment of PTPN11 to the complex are essential for FGF1 signaling. Induces the phosphorylation and activation of FGFR1, FRS2, MAPK3/ERK1, MAPK1/ERK2 and AKT1 (PubMed:18441324, PubMed:20422052). Can induce angiogenesis (PubMed:23469107). {ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:18441324, ECO:0000269|PubMed:20145243, ECO:0000269|PubMed:20422052, ECO:0000269|PubMed:23469107, ECO:0000269|PubMed:8663044}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Melanoma - Homo sapiens (human);Breast cancer - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Angiogenesis overview;Differentiation Pathway;Lung fibrosis;MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Endometrial cancer;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;FGFR2b ligand binding and activation;FGFR2c ligand binding and activation;FGFR2 ligand binding and activation;FRS-mediated FGFR2 signaling;Negative regulation of FGFR2 signaling;Signaling by FGFR2;FGFR3b ligand binding and activation;Phospholipase C-mediated cascade; FGFR2;FGFR3c ligand binding and activation;SHC-mediated cascade:FGFR2;FRS-mediated FGFR3 signaling;PI-3K cascade:FGFR2;Downstream signaling of activated FGFR2;SHC-mediated cascade:FGFR3;PI-3K cascade:FGFR4;PI-3K cascade:FGFR3;Downstream signaling of activated FGFR3;Disease;Negative regulation of FGFR3 signaling;Signaling by FGFR3;FGFR4 ligand binding and activation;Signal Transduction;FRS-mediated FGFR4 signaling;SHC-mediated cascade:FGFR4;Downstream signaling of activated FGFR4;Negative regulation of FGFR4 signaling;Signaling by FGFR4;Signaling by FGFR;FGFR3 ligand binding and activation;FGFR3 mutant receptor activation;PI3K Cascade;IRS-mediated signalling;Insulin receptor signalling cascade;Activated point mutants of FGFR2;Signaling by Insulin receptor;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Signaling by FGFR2 IIIa TM;FGF;Signaling by FGFR2 in disease;Fibroblast growth factor-1;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Signaling by activated point mutants of FGFR3;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;PIP3 activates AKT signaling;Posttranslational regulation of adherens junction stability and dissassembly;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;FGFR2 mutant receptor activation;Signaling by FGFR3 point mutants in cancer;Signaling by FGFR3 in disease;Signaling by FGFR in disease;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;GPCR signaling-G alpha i;IRS-related events triggered by IGF1R;IGF1R signaling cascade;Signaling by activated point mutants of FGFR1;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Signaling by Receptor Tyrosine Kinases;Intracellular signaling by second messengers;Phospholipase C-mediated cascade: FGFR1;Diseases of signal transduction;Syndecan-1-mediated signaling events;FGFR1b ligand binding and activation;Downstream signaling of activated FGFR1;Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R);FGFR1c ligand binding and activation;FGF signaling pathway;FGFR1 ligand binding and activation;Syndecan-2-mediated signaling events;Syndecan-3-mediated signaling events;FRS-mediated FGFR1 signaling;SHC-mediated cascade:FGFR1;PI-3K cascade:FGFR1;Negative regulation of FGFR1 signaling;Signaling by FGFR1;Phospholipase C-mediated cascade; FGFR3;Phospholipase C-mediated cascade; FGFR4
(Consensus)
Recessive Scores
- pRec
- 0.952
Intolerance Scores
- loftool
- 0.258
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.95
Haploinsufficiency Scores
- pHI
- 0.908
- hipred
- Y
- hipred_score
- 0.767
- ghis
- 0.532
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fgf1
- Phenotype
- homeostasis/metabolism 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); hematopoietic system phenotype; normal phenotype;
Zebrafish Information Network
- Gene name
- fgf1a
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- kinked
Gene ontology
- Biological process
- MAPK cascade;activation of MAPK activity;angiogenesis;organ induction;signal transduction;multicellular organism development;cell population proliferation;positive regulation of cell population proliferation;fibroblast growth factor receptor signaling pathway;anatomical structure morphogenesis;regulation of signaling receptor activity;positive regulation of endothelial cell migration;peptidyl-tyrosine phosphorylation;cell differentiation;lung development;positive regulation of cell migration;activation of protein kinase B activity;cellular response to heat;phosphatidylinositol-3-phosphate biosynthetic process;positive regulation of MAP kinase activity;positive regulation of cholesterol biosynthetic process;positive regulation of angiogenesis;positive regulation of transcription by RNA polymerase II;phosphatidylinositol phosphorylation;positive regulation of epithelial cell proliferation;positive regulation of cell division;positive regulation of protein kinase B signaling;branch elongation involved in ureteric bud branching;mesonephric epithelium development;regulation of endothelial tube morphogenesis;positive regulation of intracellular signal transduction;positive regulation of sprouting angiogenesis;regulation of endothelial cell chemotaxis to fibroblast growth factor
- Cellular component
- extracellular region;extracellular space;nucleolus;cytosol;cell cortex;extracellular matrix
- Molecular function
- protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;fibroblast growth factor receptor binding;integrin binding;protein binding;growth factor activity;heparin binding;1-phosphatidylinositol-3-kinase activity;Hsp70 protein binding;S100 protein binding;phosphatidylinositol-4,5-bisphosphate 3-kinase activity