FOXG1
forkhead box G1, the group of Forkhead boxes
Basic information
Region (hg38): 14:28764329-28770277
Previous symbols: [ "FKHL2", "FOXG1B", "FKHL4", "FKH2", "FKHL1", "FOXG1C", "FKHL3", "FOXG1A" ]
Links
Phenotypes
GenCC
Source:
- FOXG1 disorder (Definitive), mode of inheritance: AD
- Rett syndrome, congenital variant (Strong), mode of inheritance: AD
- Rett syndrome, congenital variant (Definitive), mode of inheritance: AD
- FOXG1 disorder (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Rett syndrome, congenital variant | 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 | 18571142; 19578037; 19564653; 20736978; 21441262; 21536641; 21910242; 21953941; 22091895; 22129046; 22258524; 22415763; 22670136 |
ClinVar
This is a list of variants' phenotypes submitted to
- Rett_syndrome,_congenital_variant (682 variants)
- not_provided (260 variants)
- Inborn_genetic_diseases (118 variants)
- FOXG1_disorder (106 variants)
- not_specified (79 variants)
- FOXG1-related_disorder (35 variants)
- Rett_syndrome (16 variants)
- Intellectual_disability (3 variants)
- Neurodevelopmental_disorder (2 variants)
- Stereotypic_movement_disorder (1 variants)
- Abnormal_cerebral_morphology (1 variants)
- Autism_spectrum_disorder (1 variants)
- Abnormal_optic_nerve_morphology (1 variants)
- Aplasia/Hypoplasia_of_the_corpus_callosum (1 variants)
- Microcephaly (1 variants)
- Severe_intellectual_deficiency (1 variants)
- Lissencephaly (1 variants)
- Axial_hypotonia (1 variants)
- Seizure (1 variants)
- Neurodevelopmental_abnormality (1 variants)
- Strabismus (1 variants)
- Global_developmental_delay (1 variants)
- See_cases (1 variants)
- Abnormality_of_the_nervous_system (1 variants)
- Intellectual_disability,_severe (1 variants)
- Combined_oxidative_phosphorylation_defect_type_24 (1 variants)
- Primary_microcephaly (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXG1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005249.5. 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 | 35 | 183 | 20 | 239 | ||
| missense | 36 | 72 | 201 | 52 | 34 | 395 |
| nonsense | 45 | 54 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 91 | 24 | 117 | |||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 173 | 105 | 239 | 235 | 54 |
Highest pathogenic variant AF is 0.00000985336
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FOXG1 | protein_coding | protein_coding | ENST00000382535 | 1 | 3821 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.944 | 0.0563 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.49 | 84 | 234 | 0.358 | 0.0000115 | 3156 |
| Missense in Polyphen | 3 | 62.181 | 0.048246 | 684 | ||
| Synonymous | -2.38 | 137 | 106 | 1.29 | 0.00000569 | 1025 |
| Loss of Function | 2.79 | 0 | 9.09 | 0.00 | 3.97e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription repression factor which plays an important role in the establishment of the regional subdivision of the developing brain and in the development of the telencephalon. {ECO:0000269|PubMed:12657635}.;
- Pathway
- FoxO signaling pathway - Homo sapiens (human);Tgif disruption of Shh signaling;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.696
Intolerance Scores
- loftool
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.404
- hipred
- hipred_score
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Foxg1
- Phenotype
- hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); normal phenotype; pigmentation phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; skeleton phenotype; digestive/alimentary 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); hearing/vestibular/ear phenotype; craniofacial phenotype; vision/eye phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); taste/olfaction phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- foxg1a
- Affected structure
- microvillous olfactory receptor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;brain development;aging;negative regulation of transcription, DNA-templated
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;sequence-specific DNA binding