FGF13
protein-codingfibroblast growth factor 13, the group of Fibroblast growth factor family|MicroRNA protein coding host genes
Gene summary
The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth, and invasion. This gene is located in a region on chromosome X, which is associated with Borjeson-Forssman-Lehmann syndrome (BFLS), making it a possible candidate gene for familial cases of the BFLS, and for other syndromal and nonspecific forms of X-linked cognitive disability mapping to this region. Alternative splicing of this gene at the 5' end results in several transcript variants encoding different isoforms with different N-termini. [provided by RefSeq, Nov 2008]
- LINC00889
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~608.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: XL
Disease ID:MONDO:0025353
Submitter: PanelApp Australia
Inheritance Pattern: XL
Disease ID:MONDO:0859086
Submitter: PanelApp Australia
Inheritance Pattern: XL
Disease ID:MONDO:0025353
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: XL
Disease ID:MONDO:0025353
Submitter: Ambry Genetics
Inheritance Pattern: XL
Disease ID:MONDO:0025353
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FGF13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004114.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | 5 | 14 | |||
| missense | 3 | 2 | 51 | 2 | 58 | |
| nonsense | 1 | 3 | 4 | |||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 4 | 2 | 71 | 7 | 0 | 84 |
Highest pathogenic variant AF is 9.1171165e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004105.1 | 5 | MANE Select | |
| Ensembl | ENSP00000322390.6 | 5 | MANE Select | |
| RefSeq | NP_001132970.1 | 5 | Standard | |
| RefSeq | NP_001132972.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
- MAPK Signaling Pathway
- PI3K-Akt Signaling Pathway
- Regulation of Actin Cytoskeleton
Biological Process
- MAPK cascade
- neuron migration
- sodium ion transport
- negative regulation of microtubule depolymerization
- signal transduction
Molecular Function
- protein binding
- microtubule binding
- growth factor activity
- sodium channel regulator activity
- protein kinase activator activity
Cellular Component
- extracellular region
- nucleus
- nucleolus
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370603
- Coding exons
- 6
- Length
- 591205
- Individuals with no LoFs
- 124263
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 3
- Defined
- 124267
- p
- 0.0000161
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 55 | 99.7 | 0.552 | 0.00000778 | 1653 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000041 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000040 | 0.000027 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- LoFtool
- 0.226
- RVIS EVS
- -0.21
- RVIS percentile EVS
- 38.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |