FGF13
fibroblast growth factor 13, the group of Fibroblast growth factor family|MicroRNA protein coding host genes
Basic information
Region (hg38): X:138614727-139222777
Previous symbols: [ "LINC00889" ]
Links
Phenotypes
GenCC
Source:
- undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
- developmental and epileptic encephalopathy, 90 (Strong), mode of inheritance: XL
- developmental and epileptic encephalopathy, 90 (Moderate), mode of inheritance: XL
- developmental and epileptic encephalopathy, 90 (Limited), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Developmental and epileptic encephalopathy 90; Intellectual developmental disorder, X-linked 110 | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 33245860; 34184986 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (24 variants)
- Developmental_and_epileptic_encephalopathy,_90 (11 variants)
- Inborn_genetic_diseases (5 variants)
- not_specified (2 variants)
- FGF13-related_disorder (2 variants)
- Neurodevelopmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGF13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004114.5. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 25 | 32 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 4 | 2 | 27 | 5 | 1 |
Highest pathogenic variant AF is 9.1171165e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FGF13 | protein_coding | protein_coding | ENST00000370603 | 6 | 591205 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.895 | 0.105 | 124263 | 1 | 3 | 124267 | 0.0000161 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 55 | 99.7 | 0.552 | 0.00000778 | 1653 |
| Missense in Polyphen | 9 | 24.672 | 0.36479 | 436 | ||
| Synonymous | 0.420 | 38 | 41.4 | 0.917 | 0.00000354 | 482 |
| Loss of Function | 2.90 | 1 | 11.7 | 0.0855 | 0.00000103 | 181 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000411 | 0.0000411 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000398 | 0.0000266 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Microtubule-binding protein which directly binds tubulin and is involved in both polymerization and stabilization of microtubules. Through its action on microtubules, may participate to the refinement of axons by negatively regulating axonal and leading processes branching. Plays a crucial role in neuron polarization and migration in the cerebral cortex and the hippocampus. {ECO:0000269|PubMed:15282281}.; FUNCTION: May also play a role in MAPK signaling. {ECO:0000269|PubMed:15282281}.;
- Pathway
- Nuclear Receptors Meta-Pathway;NRF2 pathway;MAPK Signaling Pathway;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;FGF;GPCR signaling-G alpha s Epac and ERK;Phase 0 - rapid depolarisation;Cardiac conduction;Muscle contraction;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i
(Consensus)
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- 0.226
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.897
- hipred
- Y
- hipred_score
- 0.702
- ghis
- 0.599
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Fgf13
- Phenotype
- cellular 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- MAPK cascade;neuron migration;sodium ion transport;negative regulation of microtubule depolymerization;signal transduction;cell-cell signaling;nervous system development;learning;memory;regulation of signaling receptor activity;hippocampus development;cerebral cortex cell migration;activation of protein kinase activity;establishment of neuroblast polarity;microtubule polymerization;negative regulation of collateral sprouting;protein localization to plasma membrane;regulation of cardiac muscle cell action potential involved in regulation of contraction
- Cellular component
- extracellular region;nucleus;nucleolus;cytoplasm;cytosol;microtubule;plasma membrane;intercalated disc;lateral plasma membrane;filopodium;axon;dendrite;growth cone;neuron projection
- Molecular function
- protein binding;microtubule binding;growth factor activity;sodium channel regulator activity;protein kinase activator activity;ion channel binding;beta-tubulin binding