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FOXP2 forkhead box P2 [ Homo sapiens (human) ]

Gene ID: 93986, updated on 16-Apr-2024

Summary

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Official Symbol
FOXP2provided by HGNC
Official Full Name
forkhead box P2provided by HGNC
Primary source
HGNC:HGNC:13875
See related
Ensembl:ENSG00000128573 MIM:605317; AllianceGenome:HGNC:13875
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPCH1; CAGH44; TNRC10
Summary
This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. It is expressed in fetal and adult brain as well as in several other organs such as the lung and gut. The protein product contains a FOX DNA-binding domain and a large polyglutamine tract and is an evolutionarily conserved transcription factor, which may bind directly to approximately 300 to 400 gene promoters in the human genome to regulate the expression of a variety of genes. This gene is required for proper development of speech and language regions of the brain during embryogenesis, and may be involved in a variety of biological pathways and cascades that may ultimately influence language development. Mutations in this gene cause speech-language disorder 1 (SPCH1), also known as autosomal dominant speech and language disorder with orofacial dyspraxia. Multiple alternative transcripts encoding different isoforms have been identified in this gene.[provided by RefSeq, Feb 2010]
Expression
Ubiquitous expression in ovary (RPKM 3.6), endometrium (RPKM 3.4) and 22 other tissues See more
Orthologs
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Genomic context

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See FOXP2 in Genome Data Viewer
Location:
7q31.1
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (114086327..114693765)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (115401144..116008457)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (113726382..114333820)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:113382595-113383179 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:113383180-113383763 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:113465760-113466396 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:113608629-113608855 Neighboring gene protein phosphatase 1 regulatory subunit 3A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26522 Neighboring gene VISTA enhancer hs720 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:113848263-113848364 Neighboring gene ribosomal protein L36 pseudogene 13 Neighboring gene VISTA enhancer hs218 Neighboring gene VISTA enhancer hs999 Neighboring gene Sharpr-MPRA regulatory region 15446 Neighboring gene VISTA enhancer hs1080 Neighboring gene VISTA enhancer hs222 Neighboring gene VISTA enhancer hs956 Neighboring gene RNA, 5S ribosomal pseudogene 238 Neighboring gene VISTA enhancer hs966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:114373209-114373709 Neighboring gene microRNA 3666 Neighboring gene VISTA enhancer hs1192 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:114465341-114466180 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26523 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18551 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18549 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:114570117-114570666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26524 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:114670265-114670880 Neighboring gene MyoD family inhibitor domain containing Neighboring gene long intergenic non-protein coding RNA 1393 Neighboring gene long intergenic non-protein coding RNA 1392

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Human-specific changes in two functional enhancers of FOXP2. BenĂ­tez-Burraco A, et al. Cell Mol Biol (Noisy-le-grand), 2022 Nov 30. PMID 37114314
  2. Functional dissection of two amino acid substitutions unique to the human FOXP2 protein. Bornschein U, et al. Sci Rep, 2023 Mar 6. PMID 36879029, Free PMC Article
  3. Investigation of the forkhead box protein P2 gene by the next-generation sequence analysis method in children diagnosed with specific learning disorder. Yazıcı M, et al. Psychiatr Genet, 2023 Feb 1. PMID 36617742
  4. In-depth characterisation of a cohort of individuals with missense and loss-of-function variants disrupting FOXP2. Morison LD, et al. J Med Genet, 2023 Jun. PMID 36328423, Free PMC Article
  5. Do variants in the coding regions of FOXP2, a gene implicated in speech disorder, confer a risk for congenital amusia? Peretz I, et al. Ann N Y Acad Sci, 2022 Nov. PMID 35980667

See all (181) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel FOXP2 variant associated with speech and language dysfunction in a Chinese family and literature review.
    Title: Novel FOXP2 variant associated with speech and language dysfunction in a Chinese family and literature review.
  2. FOXP2 suppresses the proliferation, invasion, and aerobic glycolysis of hepatocellular carcinoma cells by regulating the KDM5A/FBP1 axis.
    Title: FOXP2 suppresses the proliferation, invasion, and aerobic glycolysis of hepatocellular carcinoma cells by regulating the KDM5A/FBP1 axis.
  3. LncRNA CERS6-AS1, sponging miR-6838-5p, promotes proliferation and invasion in cervical carcinoma cells by upregulating FOXP2.
    Title: LncRNA CERS6-AS1, sponging miR-6838-5p, promotes proliferation and invasion in cervical carcinoma cells by upregulating FOXP2.
  4. In-depth characterisation of a cohort of individuals with missense and loss-of-function variants disrupting FOXP2.
    Title: In-depth characterisation of a cohort of individuals with missense and loss-of-function variants disrupting FOXP2.
  5. Human-specific changes in two functional enhancers of FOXP2.
    Title: Human-specific changes in two functional enhancers of FOXP2.
  6. Functional dissection of two amino acid substitutions unique to the human FOXP2 protein.
    Title: Functional dissection of two amino acid substitutions unique to the human FOXP2 protein.
  7. Dissecting the cross-trait effects of the FOXP2 GWAS hit on clinical and brain phenotypes in adults with ADHD.
    Title: Dissecting the cross-trait effects of the FOXP2 GWAS hit on clinical and brain phenotypes in adults with ADHD.
  8. Investigation of the forkhead box protein P2 gene by the next-generation sequence analysis method in children diagnosed with specific learning disorder.
    Title: Investigation of the forkhead box protein P2 gene by the next-generation sequence analysis method in children diagnosed with specific learning disorder.
  9. Silencing FOXP2 reverses vemurafenib resistance in BRAF[V600E] mutant papillary thyroid cancer and melanoma cells.
    Title: Silencing FOXP2 reverses vemurafenib resistance in BRAF(V600E) mutant papillary thyroid cancer and melanoma cells.
  10. Do variants in the coding regions of FOXP2, a gene implicated in speech disorder, confer a risk for congenital amusia?
    Title: Do variants in the coding regions of FOXP2, a gene implicated in speech disorder, confer a risk for congenital amusia?
Submit: New GeneRIF Correction See all GeneRIFs (130)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Childhood apraxia of speech
MedGen: C0750927 OMIM: 602081 GeneReviews: FOXP2-Related Speech and Language Disorder
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2012-09-19)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2012-09-19)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300.
EBI GWAS Catalog
Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat specifically associates with FOXP2 promoter to upregulate FOXP2 expression in T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp686H1726

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in caudate nucleus development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cerebral cortex development IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in putamen development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
forkhead box protein P2
Names
CAG repeat protein 44
forkhead/winged-helix transcription factor
trinucleotide repeat containing 10
trinucleotide repeat-containing gene 10 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007491.3 RefSeqGene

    Range
    333506..612456
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001172766.3 → NP_001166237.1  forkhead box protein P2 isoform V

    See identical proteins and their annotated locations for NP_001166237.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an in-frame exon and uses an alternate in-frame splice site in the coding region, compared to variant 2. The resulting isoform (V) is shorter than isoform II.
    Source sequence(s)
    AC020606, AC073626, AF337817, AI369947, BC018016, BC143867
    UniProtKB/TrEMBL
    A0A0U1RQM2
    Related
    ENSP00000377135.2, ENST00000393498.6
    Conserved Domains (2) summary
    cd00059
    Location:503 → 575
    FH; Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as ...
    pfam16159
    Location:341 → 408
    FOXP-CC; FOXP coiled-coil domain

  2. NM_001172767.2 → NP_001166238.1  forkhead box protein P2 isoform VI

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, the 3' coding region and the 3' UTR, compared to variant 2. The resulting isoform (VI) has a distinct C-terminus and is shorter than isoform II.
    Source sequence(s)
    AF337817, AF467254, AF467259
    UniProtKB/TrEMBL
    Q8N6B5
    Related
    ENSP00000375084.3, ENST00000390668.3
    Conserved Domains (1) summary
    pfam16159
    Location:367 → 434
    FOXP-CC; FOXP coiled-coil domain

  3. NM_014491.4 → NP_055306.1  forkhead box protein P2 isoform I

    See identical proteins and their annotated locations for NP_055306.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the 5' coding region, as compared to variant 2. The resulting isoform (I) is shorter than isoform II.
    Source sequence(s)
    AC020606, AC073626, AF337817, AI369947, BC018016
    Consensus CDS
    CCDS5760.1
    UniProtKB/Swiss-Prot
    A0AUV6, A4D0U8, A6NNW4, B4DLD9, O15409, Q6ZND1, Q75MJ3, Q8IZE0, Q8N0W2, Q8N6B7, Q8N6B8, Q8NFQ1, Q8NFQ2, Q8NFQ3, Q8NFQ4, Q8TD74
    UniProtKB/TrEMBL
    A0A0U1RQM2
    Related
    ENSP00000265436.7, ENST00000350908.9
    Conserved Domains (2) summary
    cd00059
    Location:504 → 576
    FH; Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as ...
    pfam16159
    Location:342 → 409
    FOXP-CC; FOXP coiled-coil domain

  4. NM_148898.4 → NP_683696.2  forkhead box protein P2 isoform II

    See identical proteins and their annotated locations for NP_683696.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (II).
    Source sequence(s)
    AC020606, AC073626, AI369947, AY144615, BC018016
    Consensus CDS
    CCDS43635.1
    UniProtKB/TrEMBL
    A4D0T4, X5D2H2
    Related
    ENSP00000386200.3, ENST00000408937.7
    Conserved Domains (2) summary
    cd00059
    Location:529 → 601
    FH; Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as ...
    pfam16159
    Location:367 → 434
    FOXP-CC; FOXP coiled-coil domain

  5. NM_148899.3 → NP_683697.2  forkhead box protein P2 isoform III

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks an in-frame exon in the 5' coding region, and differs in the 3' coding region and 3' UTR, compared to variant 2. The resulting isoform (III) has a distinct C-terminus and is shorter than isoform II.
    Source sequence(s)
    AF467253, AF467254, AF467258
    Consensus CDS
    CCDS5761.2
    UniProtKB/TrEMBL
    Q8N6B6
    Related
    ENSP00000353367.4, ENST00000360232.8
    Conserved Domains (1) summary
    pfam16159
    Location:342 → 409
    FOXP-CC; FOXP coiled-coil domain

  6. NM_148900.4 → NP_683698.2  forkhead box protein P2 isoform IV

    See identical proteins and their annotated locations for NP_683698.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon and has an additional in-frame exon in the coding region, compared to variant 2. The resulting isoform (IV) is shorter than isoform II.
    Source sequence(s)
    AC020606, AC073626, AI369947, AK296957, BC018016
    Consensus CDS
    CCDS55154.1
    UniProtKB/TrEMBL
    A0A0U1RQY3
    Related
    ENSP00000385069.4, ENST00000403559.9
    Conserved Domains (2) summary
    cd00059
    Location:521 → 593
    FH; Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as ...
    pfam16159
    Location:359 → 426
    FOXP-CC; FOXP coiled-coil domain

RNA

  1. NR_033766.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) has multiple differences compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC020606, AI369947, AK131266, DA400243

  2. NR_033767.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) has multiple differences compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC020606, AC073626, AI369947, BC018016, BC143866

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    114086327..114693765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    115401144..116008457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15409.2 GenPept UniProtKB/Swiss-Prot:O15409

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