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Aliases for FOXG1 Gene

Aliases for FOXG1 Gene

  • Forkhead Box G1 2 3 5
  • Brain Factor 1 2 3 4
  • Brain Factor 2 3 4
  • FOXG1A 3 4
  • FOXG1B 3 4
  • FOXG1C 3 4
  • HBF-2 3 4
  • FKHL1 3 4
  • FKHL2 3 4
  • FKHL3 3 4
  • FKHL4 3 4
  • FKH2 3 4
  • HFK1 3 4
  • HFK2 3 4
  • HFK3 3 4
  • BF1 3 4
  • BF2 3 4
  • Forkhead-Related Protein FKHL1 4
  • Forkhead-Related Protein FKHL2 4
  • Forkhead-Related Protein FKHL3 4
  • Forkhead Box Protein G1A 4
  • Forkhead Box Protein G1B 4
  • Forkhead Box Protein G1C 4
  • Forkhead Box Protein G1 3
  • Forkhead Box G1B 2
  • Forkhead Box G1C 2
  • Forkhead Box G1A 2
  • Forkhead-Like 1 3
  • Forkhead-Like 2 3
  • Forkhead-Like 3 3
  • Forkhead-Like 4 3
  • Oncogene QIN 3
  • HBF-G2 3
  • FHKL3 3
  • HBF-1 3
  • HBF-3 3
  • HBF2 3
  • KHL2 3
  • BF-1 4
  • BF-2 4
  • QIN 3

External Ids for FOXG1 Gene

Previous HGNC Symbols for FOXG1 Gene

  • FKHL2
  • FOXG1B
  • FKHL4
  • FKH2
  • FKHL1
  • FOXG1C
  • FKHL3
  • FOXG1A

Previous GeneCards Identifiers for FOXG1 Gene

  • GC14P028306
  • GC14P029235
  • GC14P009354

Summaries for FOXG1 Gene

Entrez Gene Summary for FOXG1 Gene

  • This locus encodes a member of the forked-head transcription factor family. The encoded protein, which functions as a repressor, may play a role in brain development. Mutations at this locus have been associated with Rett syndrome. [provided by RefSeq, Feb 2012]

GeneCards Summary for FOXG1 Gene

FOXG1 (Forkhead Box G1) is a Protein Coding gene. Diseases associated with FOXG1 include Rett Syndrome, Congenital Variant and Rett Syndrome. Among its related pathways are FoxO signaling pathway and Regulation of nuclear SMAD2/3 signaling. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is FOXD2.

UniProtKB/Swiss-Prot for FOXG1 Gene

  • 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.

Gene Wiki entry for FOXG1 Gene

Additional gene information for FOXG1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FOXG1 Gene

Genomics for FOXG1 Gene

GeneHancer (GH) Regulatory Elements for FOXG1 Gene

Promoters and enhancers for FOXG1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J028759 Enhancer 0.8 FANTOM5 ENCODE dbSUPER 659.7 -0.8 -779 0.3 MAFK EZH2 FOXG1 FOXG1-AS1 BTF3P2
GH14J028761 Enhancer 0.5 dbSUPER 650.7 +1.7 1728 2 POLR2A CEBPA ATF7 EZH2 FOXG1 FOXG1-AS1
GH14J028760 Enhancer 0.4 dbSUPER 650.7 -0.2 -197 0.2 POLR2A SUZ12 EZH2 FOXG1 FOXG1-AS1 BTF3P2
GH14J028762 Enhancer 0.3 dbSUPER 650.7 -1.1 -1143 0.2 EZH2 FOXG1 FOXG1-AS1 BTF3P2
GH14J028774 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 23.8 +14.4 14413 0.5 CTCF SUZ12 RAD21 ZNF2 POLR2A PRDM10 ZNF600 EZH2 ZBTB20 ZNF654 FOXG1 LINC01551 LINC02282
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FOXG1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FOXG1 gene promoter:
  • FOXO4
  • POU2F1
  • HFH-1
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)

Genomic Locations for FOXG1 Gene

Genomic Locations for FOXG1 Gene
9,948 bases
Plus strand
3,822 bases
Plus strand

Genomic View for FOXG1 Gene

Genes around FOXG1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FOXG1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FOXG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FOXG1 Gene

Proteins for FOXG1 Gene

  • Protein details for FOXG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Forkhead box protein G1
    Protein Accession:
    Secondary Accessions:
    • A6NFY2
    • P55315
    • Q14488
    • Q86XT7

    Protein attributes for FOXG1 Gene

    489 amino acids
    Molecular mass:
    52352 Da
    Quaternary structure:
    • Interacts with KDM5B.

neXtProt entry for FOXG1 Gene

Post-translational modifications for FOXG1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FOXG1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FOXG1 Gene

Domains & Families for FOXG1 Gene

Gene Families for FOXG1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for FOXG1 Gene

Suggested Antigen Peptide Sequences for FOXG1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FOXG1: view

No data available for UniProtKB/Swiss-Prot for FOXG1 Gene

Function for FOXG1 Gene

Molecular function for FOXG1 Gene

UniProtKB/Swiss-Prot 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.

LifeMap Function Summary for FOXG1 Gene

FOXG1 as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells:

Phenotypes From GWAS Catalog for FOXG1 Gene

Gene Ontology (GO) - Molecular Function for FOXG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS,IBA 19274049
GO:0003677 DNA binding TAS 7957066
GO:0003700 DNA binding transcription factor activity IEA --
GO:0005515 protein binding IPI 12657635
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with FOXG1: view
genes like me logo Genes that share phenotypes with FOXG1: view

Human Phenotype Ontology for FOXG1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FOXG1 Gene

MGI Knock Outs for FOXG1:

Animal Model Products

Clone Products

  • Addgene plasmids for FOXG1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for FOXG1 Gene

Localization for FOXG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXG1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FOXG1 gene
Compartment Confidence
nucleus 5
extracellular 1
mitochondrion 1
cytosol 1

Gene Ontology (GO) - Cellular Components for FOXG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with FOXG1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for FOXG1 Gene

Pathways & Interactions for FOXG1 Gene

genes like me logo Genes that share pathways with FOXG1: view

Pathways by source for FOXG1 Gene

1 KEGG pathway for FOXG1 Gene
1 GeneGo (Thomson Reuters) pathway for FOXG1 Gene

SIGNOR curated interactions for FOXG1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for FOXG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0002052 positive regulation of neuroblast proliferation IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA,IEA --
genes like me logo Genes that share ontologies with FOXG1: view

Drugs & Compounds for FOXG1 Gene

No Compound Related Data Available

Transcripts for FOXG1 Gene

mRNA/cDNA for FOXG1 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(9) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for FOXG1 Gene

Forkhead box G1:
Representative Sequences:

Clone Products

  • Addgene plasmids for FOXG1

Alternative Splicing Database (ASD) splice patterns (SP) for FOXG1 Gene

No ASD Table

Relevant External Links for FOXG1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FOXG1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FOXG1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FOXG1 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x6.5), Brain - Cortex (x6.5), Brain - Anterior cingulate cortex (BA24) (x6.4), Brain - Nucleus accumbens (basal ganglia) (x6.1), Brain - Putamen (basal ganglia) (x5.8), Brain - Caudate (basal ganglia) (x5.7), Brain - Hippocampus (x5.6), and Brain - Amygdala (x5.2).

Protein differential expression in normal tissues from HIPED for FOXG1 Gene

This gene is overexpressed in Fetal Brain (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for FOXG1 Gene

Protein tissue co-expression partners for FOXG1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of FOXG1 Gene:


SOURCE GeneReport for Unigene cluster for FOXG1 Gene:


mRNA Expression by UniProt/SwissProt for FOXG1 Gene:

Tissue specificity: Expression is restricted to the neurons of the developing telencephalon.

Evidence on tissue expression from TISSUES for FOXG1 Gene

  • Nervous system(4.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FOXG1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • salivary gland
  • skull
  • tongue
  • tooth
  • vocal cord
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • intestine
  • large intestine
  • stomach
  • pelvis
  • rectum
  • arm
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with FOXG1: view

Orthologs for FOXG1 Gene

This gene was present in the common ancestor of animals.

Orthologs for FOXG1 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia FOXG1 34
  • 100 (a)
(Pan troglodytes)
Mammalia FOXG1 34 33
  • 99.29 (n)
(Bos Taurus)
Mammalia FOXG1 33
  • 95.57 (n)
(Mus musculus)
Mammalia Foxg1 16 34 33
  • 93.9 (n)
(Rattus norvegicus)
Mammalia Foxg1 33
  • 93.89 (n)
(Ornithorhynchus anatinus)
Mammalia FOXG1 34
  • 92 (a)
(Monodelphis domestica)
Mammalia FOXG1 34
  • 91 (a)
(Gallus gallus)
Aves FOXG1 34
  • 93 (a)
(Anolis carolinensis)
Reptilia FOXG1 34
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia foxg1 33
  • 82.64 (n)
African clawed frog
(Xenopus laevis)
Amphibia foxg1b-A-prov 33
(Danio rerio)
Actinopterygii foxg1a 34 33
  • 75 (n)
foxg1 33
fruit fly
(Drosophila melanogaster)
Insecta slp1 34
  • 34 (a)
slp2 34
  • 33 (a)
fd19B 34
  • 31 (a)
(Caenorhabditis elegans)
Secernentea fkh-2 34
  • 43 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 30 (a)
Species where no ortholog for FOXG1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for FOXG1 Gene

Gene Tree for FOXG1 (if available)
Gene Tree for FOXG1 (if available)
Evolutionary constrained regions (ECRs) for FOXG1: view image

Paralogs for FOXG1 Gene

(1) SIMAP similar genes for FOXG1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with FOXG1: view

Variants for FOXG1 Gene

Sequence variations from dbSNP and Humsavar for FOXG1 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1057516138 likely-pathogenic, Rett syndrome, congenital variant 28,767,833(+) G/T coding_sequence_variant, missense_variant
rs1057524328 likely-benign, not specified, Rett syndrome, congenital variant 28,768,599(+) C/G coding_sequence_variant, synonymous_variant
rs1064797186 uncertain-significance, likely-pathogenic, not provided, Rett syndrome, congenital variant 28,767,964(+) A/C coding_sequence_variant, missense_variant
rs112803404 conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign, not specified, not provided, Rett syndrome, congenital variant 28,767,726(+) C/G/T coding_sequence_variant, synonymous_variant
rs121913678 pathogenic, Rett syndrome, congenital variant 28,768,044(+) G/A/T coding_sequence_variant, missense_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for FOXG1 Gene

Variant ID Type Subtype PubMed ID
dgv1059n106 CNV deletion 24896259
nsv1071138 CNV deletion 25765185
nsv1227 CNV insertion 18451855
nsv520282 CNV loss 19592680
nsv526536 CNV gain 19592680
nsv826911 CNV gain 20364138

Variation tolerance for FOXG1 Gene

Residual Variation Intolerance Score: 31.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.55; 11.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FOXG1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXG1 Gene

Disorders for FOXG1 Gene

MalaCards: The human disease database

(15) MalaCards diseases for FOXG1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
rett syndrome, congenital variant
  • rett syndrome congenital variant
rett syndrome
  • rtt
14q12 microdeletion syndrome
  • del(14)(q12)
14q11.2 microduplication syndrome
  • dup(14)(q11.2)
foxg1 syndrome
  • foxg1-related disorder
- elite association - COSMIC cancer census association via MalaCards
Search FOXG1 in MalaCards View complete list of genes associated with diseases


  • Rett syndrome congenital variant (RTTCV) [MIM:613454]: A severe neurodevelopmental disorder with features of classic Rett syndrome but earlier onset in the first months of life. Clinical features include progressive microcephaly, hypotonia, irresponsiveness and irritability in the neonatal period, mental retardation, psychomotor regression and stereotypical movements. {ECO:0000269 PubMed:19578037, ECO:0000269 PubMed:21280142, ECO:0000269 PubMed:26993267}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for FOXG1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FOXG1: view

No data available for Genatlas for FOXG1 Gene

Publications for FOXG1 Gene

  1. Human brain factor 1, a new member of the fork head gene family. (PMID: 7959731) Murphy DB … Thies U (Genomics 1994) 2 3 4 22 58
  2. Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation. (PMID: 17260156) Bredenkamp N … Illing N (Development genes and evolution 2007) 2 3 4 58
  3. Human PLU-1 Has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9. (PMID: 12657635) Tan K … Freemont PS (The Journal of biological chemistry 2003) 3 4 22 58
  4. The genes for human brain factor 1 and 2, members of the fork head gene family, are clustered on chromosome 14q. (PMID: 7599184) Wiese S … Thies U (Biochimica et biophysica acta 1995) 3 4 22 58
  5. A missense mutation within the fork-head domain of the forkhead box G1 Gene (FOXG1) affects its nuclear localization. (PMID: 21280142) Le Guen T … Bienvenu T (Human mutation 2011) 3 4 58

Products for FOXG1 Gene

Sources for FOXG1 Gene

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