FGF12
Basic information
Region (hg38): 3:192139390-192767764
Previous symbols: [ "FGF12B" ]
Links
Phenotypes
GenCC
Source:
- developmental and epileptic encephalopathy, 47 (Moderate), mode of inheritance: AD
- undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
- developmental and epileptic encephalopathy, 47 (Strong), mode of inheritance: AD
- developmental and epileptic encephalopathy (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Developmental and epileptic encephalopathy 47 | AD | 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 | 27164707 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
- Seizure (1 variants)
- Early onset epileptic encephalopathy (1 variants)
- Developmental and epileptic encephalopathy, 47 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FGF12 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 | 37 | 40 | ||||
missense | 59 | 12 | 82 | |||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 2 | 9 | 8 | 19 | ||
non coding | 32 | 34 | 69 | |||
Total | 1 | 4 | 67 | 81 | 44 |
Variants in FGF12
This is a list of pathogenic ClinVar variants found in the FGF12 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-192143732-A-G | Benign (Sep 04, 2018) | |||
3-192144014-T-C | Uncertain significance (May 21, 2023) | |||
3-192144016-G-C | Uncertain significance (Nov 27, 2023) | |||
3-192144040-C-A | Uncertain significance (Jul 25, 2023) | |||
3-192144042-A-C | Uncertain significance (Jun 07, 2023) | |||
3-192144044-T-C | Uncertain significance (Apr 18, 2022) | |||
3-192144049-G-A | Uncertain significance (Aug 20, 2022) | |||
3-192144064-C-T | Developmental and epileptic encephalopathy, 47 | Uncertain significance (Aug 13, 2021) | ||
3-192144071-T-A | Uncertain significance (Dec 18, 2023) | |||
3-192144076-C-T | Uncertain significance (Mar 08, 2024) | |||
3-192144077-G-A | Uncertain significance (Dec 06, 2023) | |||
3-192144078-C-G | Likely benign (Nov 15, 2022) | |||
3-192144080-C-G | Benign (Nov 15, 2023) | |||
3-192144089-C-T | Inborn genetic diseases | Uncertain significance (Sep 02, 2024) | ||
3-192144092-C-T | Benign (Oct 17, 2022) | |||
3-192144098-C-T | Developmental and epileptic encephalopathy, 47 | Uncertain significance (Jun 22, 2023) | ||
3-192144100-T-G | Uncertain significance (Dec 24, 2022) | |||
3-192144100-TG-T | Likely pathogenic (Jun 06, 2023) | |||
3-192144105-C-T | Likely benign (Jul 01, 2024) | |||
3-192144106-G-A | Uncertain significance (Aug 20, 2023) | |||
3-192144124-C-A | Uncertain significance (Oct 25, 2022) | |||
3-192144126-C-T | FGF12-related disorder | Benign (Jan 17, 2024) | ||
3-192144144-C-A | Likely benign (Dec 24, 2020) | |||
3-192144144-C-T | Likely benign (Apr 10, 2023) | |||
3-192144401-AC-A | Benign (Mar 16, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FGF12 | protein_coding | protein_coding | ENST00000454309 | 5 | 628370 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.623 | 0.376 | 125742 | 0 | 4 | 125746 | 0.0000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.52 | 91 | 142 | 0.640 | 0.00000718 | 1571 |
Missense in Polyphen | 16 | 46.389 | 0.34491 | 528 | ||
Synonymous | 0.453 | 50 | 54.2 | 0.922 | 0.00000279 | 478 |
Loss of Function | 2.63 | 2 | 11.7 | 0.171 | 5.83e-7 | 141 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.00000928 | 0.00000879 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in nervous system development and function. Involved in the positive regulation of voltage-gated sodium channel activity. Promotes neuronal excitability by elevating the voltage dependence of neuronal sodium channel SCN8A fast inactivation. {ECO:0000269|PubMed:27164707}.;
- Pathway
- MAPK Signaling Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Regulation of Actin Cytoskeleton;Phase 0 - rapid depolarisation;Cardiac conduction;Muscle contraction
(Consensus)
Recessive Scores
- pRec
- 0.174
Intolerance Scores
- loftool
- 0.209
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.908
- hipred
- Y
- hipred_score
- 0.697
- ghis
- 0.563
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fgf12
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- regulation of membrane depolarization;signal transduction;cell-cell signaling;chemical synaptic transmission;nervous system development;heart development;adult locomotory behavior;fibroblast growth factor receptor signaling pathway;regulation of signaling receptor activity;positive regulation of sodium ion transport;neuromuscular process;cardiac muscle cell action potential involved in contraction;regulation of neuronal action potential;regulation of sodium ion transmembrane transport;regulation of voltage-gated sodium channel activity;regulation of sodium ion transmembrane transporter activity;negative regulation of cation channel activity
- Cellular component
- extracellular space;nucleus
- Molecular function
- protein binding;growth factor activity;sodium channel regulator activity;ion channel binding