FGF4
fibroblast growth factor 4, the group of Receptor ligands|Fibroblast growth factor family
Basic information
Region (hg38): 11:69771022-69775341
Previous symbols: [ "HSTF1" ]
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 FGF4 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 | 1 | |||||
| missense | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 2 | 0 |
Variants in FGF4
This is a list of pathogenic ClinVar variants found in the FGF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-69773319-G-T | Uncertain significance (Mar 29, 2021) | |||
| 11-69773436-T-A | not specified | Uncertain significance (Jul 26, 2022) | ||
| 11-69773450-A-C | not specified | Uncertain significance (Feb 10, 2022) | ||
| 11-69773463-G-A | not specified | Uncertain significance (Apr 06, 2022) | ||
| 11-69773473-C-T | not specified | Uncertain significance (Mar 29, 2022) | ||
| 11-69774016-G-A | Benign (Aug 16, 2018) | |||
| 11-69774751-G-C | not specified | Uncertain significance (Apr 18, 2023) | ||
| 11-69774792-G-A | not specified | Likely benign (Jan 29, 2024) | ||
| 11-69774827-G-C | not specified | Likely benign (Dec 08, 2023) | ||
| 11-69774864-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 11-69774948-C-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 11-69774963-G-A | not specified | Uncertain significance (Jan 16, 2024) | ||
| 11-69775002-C-T | not specified | Uncertain significance (Nov 27, 2023) | ||
| 11-69775021-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 11-69775072-C-G | not specified | Uncertain significance (Oct 27, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FGF4 | protein_coding | protein_coding | ENST00000168712 | 3 | 2375 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.141 | 0.787 | 125710 | 0 | 8 | 125718 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.00 | 69 | 96.8 | 0.713 | 0.00000522 | 1267 |
| Missense in Polyphen | 30 | 42.826 | 0.70051 | 506 | ||
| Synonymous | 0.0914 | 45 | 45.8 | 0.983 | 0.00000283 | 440 |
| Loss of Function | 1.45 | 2 | 5.77 | 0.347 | 3.32e-7 | 74 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000116 | 0.000116 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000269 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. Required for normal limb and cardiac valve development during embryogenesis. {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);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Differentiation Pathway;MECP2 and Associated Rett Syndrome;MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;FGFR2c ligand binding and activation;FGFR2 ligand binding and activation;FRS-mediated FGFR2 signaling;Negative regulation of FGFR2 signaling;Signaling by FGFR2;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;FGF;Signaling by FGFR2 in disease;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;Regulation of nuclear beta catenin signaling and target gene transcription;Phospholipase C-mediated cascade: FGFR1;Diseases of signal transduction;Syndecan-1-mediated signaling events;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;FGFRL1 modulation of FGFR1 signaling;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
- 0.609
Haploinsufficiency Scores
- pHI
- 0.388
- hipred
- Y
- hipred_score
- 0.813
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.146
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fgf4
- Phenotype
- cellular phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype; 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); reproductive system phenotype; embryo phenotype;
Zebrafish Information Network
- Gene name
- fgf4
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- bent
Gene ontology
- Biological process
- MAPK cascade;cartilage condensation;signal transduction;cell-cell signaling;positive regulation of cell population proliferation;fibroblast growth factor receptor signaling pathway;mesenchymal cell proliferation;regulation of signaling receptor activity;peptidyl-tyrosine phosphorylation;stem cell population maintenance;embryonic hindlimb morphogenesis;phosphatidylinositol-3-phosphate biosynthetic process;odontogenesis of dentin-containing tooth;negative regulation of apoptotic process;positive regulation of transcription by RNA polymerase II;phosphatidylinositol phosphorylation;positive regulation of cell division;positive regulation of protein kinase B signaling;cranial suture morphogenesis;apoptotic process involved in morphogenesis;chondroblast differentiation;positive regulation of ERK1 and ERK2 cascade;cellular response to leukemia inhibitory factor;regulation of endothelial cell chemotaxis to fibroblast growth factor
- Cellular component
- extracellular region
- Molecular function
- protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;fibroblast growth factor receptor binding;growth factor activity;heparin binding;1-phosphatidylinositol-3-kinase activity;phosphatidylinositol-4,5-bisphosphate 3-kinase activity