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    FOXP2 forkhead box P2 [ Homo sapiens (human) ]

    Gene ID: 93986, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (114086327..114693765)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (115401144..116008457)
    RS_2024_09 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 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. Downregulation of FOXP2 promoter human hepatocellular carcinoma cell invasion. Yan X, et al. Tumour Biol, 2015 Dec. PMID 26142732
    2. Mosaic 7q31 deletion involving FOXP2 gene associated with language impairment. Palka C, et al. Pediatrics, 2012 Jan. PMID 22144704
    3. A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Maricic T, et al. Mol Biol Evol, 2013 Apr. PMID 23197593
    4. Strong expression of the neuronal transcription factor FOXP2 is linked to an increased risk of early PSA recurrence in ERG fusion-negative cancers. Stumm L, et al. J Clin Pathol, 2013 Jul. PMID 23559350
    5. FOXP2 variation modulates functional hemispheric asymmetries for speech perception. Ocklenburg S, et al. Brain Lang, 2013 Sep. PMID 23911943

    See all (183) 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
    located_in 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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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