Alternative titles; symbols
HGNC Approved Gene Symbol: FOXP1
Cytogenetic location: 3p13 Genomic coordinates (GRCh38) : 3:70,954,708-71,583,978 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 3p13 | Intellectual developmental disorder with language impairment with or without autistic features | 613670 | Autosomal dominant | 3 |
FOXP1 is a transcriptional repressor that plays a critical role in monocyte differentiation and macrophage function (Shi et al., 2008).
Li and Tucker (1993) cloned a glutamine-rich factor, which they designated QRF1, that was expressed preferentially at the terminal differentiation stage of B cells and in skeletal muscle. The deduced 707-amino acid QRF1 protein contains an 84-amino acid segment that shows significant sequence homology with the DNA-binding domains of the hepatocyte nuclear factor-3/forkhead (see FOXA1; 602294) family of proteins.
By expression cloning using blood and testis cDNA libraries to identify the target of a monoclonal antibody (JC12), Banham et al. (2001) obtained a full-length cDNA encoding FOXP1. The predicted 677-amino acid protein contains coiled-coil, glutamine-rich, and serine/threonine-rich domains in its N-terminal half; a central zinc finger domain; and coiled-coil, serine/threonine/proline-rich, winged helix, and acidic domains in its C-terminal half. FOXP1 also has numerous putative phosphorylation sites, 2 nuclear localization signals (NLSs) in its C-terminal half, and 2 PEST motif in its C-terminal acidic region. Multiple-tissue array analysis showed ubiquitous expression of FOXP1 in normal adult and fetal tissues, with highest expression in lymphoid and gastrointestinal tissues. Immunohistochemistry showed that FOXP1 protein was widely expressed, with a predominantly nuclear localization, in normal tissues.
Wang et al. (2003) stated that there are 4 splice variants of mouse Foxp1, designated Foxp1a through Foxp1d. They identified and cloned Foxp1d, which encodes a Foxp1 isoform lacking the N-terminal polyglutamine domain found in Foxp1a and Foxp1b. Northern blot analysis and RNase protection assays showed tissue-specific expression of all 4 variants in mouse. Northern blot analysis of human tissues detected tissue-specific expression of FOXP1 variants, with highest levels in peripheral blood lymphocytes and in caudate nucleus of brain. Western blot analysis detected variable expression of Foxp1a, Foxp1c, and Foxp1d in mouse tissues, with high expression of all 3 isoforms in lung.
Wang et al. (2003) found that mouse Foxp1a, Foxp1c, Foxp1d, and the related Foxp2 (605317) protein bound a 7-nucleotide core sequence, TATTT(G/A)T. These Foxp proteins repressed gene transcription via binding to this consensus site, which was identified within the SV40 and IL2 (147680) promoters. In some cases, the strength of Foxp1 repression was mediated by the polyglutamine domain. Mouse Foxp1 proteins also formed homodimers or heterodimers with subfamily members, and the conserved C2H2 zinc finger and leucine zipper motifs mediated dimerization.
Using genetic manipulations, Rousso et al. (2008) demonstrated that Foxp1 established the pattern of LIM-homeodomain protein (see 601999) expression in embryonic mice and, accordingly, organized motor axon projections, their connectivity with peripheral targets, and the establishment of motor pools. Hox proteins (see 142950) dictated the pattern of Foxp1 expression in spinal cord, and both Foxp1 and Hox were required for segment-appropriate generation of motor columns and pools in mouse.
Shi et al. (2008) generated transgenic mice overexpressing human FOXP1 in monocyte/macrophage lineage cells. Circulating blood monocytes from these mice had reduced expression of macrophage colony-stimulating factor receptor (CSF1R; 164770), impaired migratory capacity, and diminished accumulation as splenic macrophages. Macrophage functions were globally impaired, and osteoclastogenesis and bone resorption were attenuated. Forced overexpression of Csf1r reversed many of the deficits, suggesting that repression of Csf1r is likely the dominant mechanism responsible for FOXP1 effects on monocyte differentiation and macrophage function.
Association of FOXP1 with Cancer
By analysis of a tumor/normal tissue expression array, Banham et al. (2001) found that expression of FOXP1 was lower in colon tumors and higher in stomach and prostate tumors compared with matched normal tissues. Immunohistochemical analysis showed frequent loss of expression, increased expression, and cytoplasmic mislocalization of the predominantly nuclear FOXP1 protein in solid tumors.
By immunohistochemical analysis of a diffuse large B-cell lymphoma (BCL) tissue microarray, Banham et al. (2005) found that untreated patients with a high percentage of FOXP1-positive nuclei had significantly reduced survival and earlier progression compared with FOXP1-negative patients.
Of 275 BCLs, Haralambieva et al. (2006) found that only 5 (3 gastrointestinal, 1 thyroid, and 1 cervical lymph node) carried a chromosomal breakpoint in the FOXP1 gene and strong nuclear FOXP1 expression. All were diffuse large BCLs rather than marginal zone BCLs. Haralambieva et al. (2006) concluded that genetic alterations at 3p13 are associated with strong FOXP1 expression.
By genomic sequence analysis, Banham et al. (2001) mapped the FOXP1 gene to chromosome 3p14.1.
Streubel et al. (2005) noted that 3 chromosomal translocations, t(11;18)(q21;q21), t(14;18)(q32;q21), and t(1;14)(p22;q32), are associated with mucosa-associated lymphoid tissue (MALT) lymphomas. They identified a t(3;14)(p14;q32) in a case of MALT lymphoma of the thyroid. FISH studies showed that the IGH locus (147100) was rearranged, and long-distance inverse PCR identified FOXP1 as the partner gene on chromosome 3. Using FISH assays to screen 91 MALT lymphomas negative for 3 common translocations, Streubel et al. (2005) identified t(3;14)(p14;q32) in 9 cases (3 thyroid, 4 ocular adnexa, and 2 skin). Most t(3;14)(p14;q32)-positive MALT lymphomas also harbored additional genetic abnormalities, such as trisomy 3. All 4 of the MALT-associated translocations were mutually exclusive. Real-time RT-PCR analysis showed upregulated expression of FOXP1 in MALT cases with t(3;14)(p14;q32) or trisomy 3. Streubel et al. (2005) concluded that FOXP1 is a translocation partner of IGH in a site-dependent subset of MALT lymphomas.
Carr et al. (2010) reported a boy with severe speech delay and delayed motor development (see 613670) who carried a de novo heterozygous 1.0-Mb interstitial deletion of chromosome 3p14.1 that involved only the FOXP1 gene. The phenotype was confounded by a Chiari I malformation, which was surgically corrected at age 30 months. The patient had delayed gross motor skills and walked at 16 months. After surgery for the Chiari malformation, he had some improvement in motor skills. The most significant feature was speech delay with limited verbal output and difficulty in articulating entire words and multisyllabic speech, although he did not have a deficit in oromotor coordination. At age 4 years, he developed staring spells with motor arrest associated with epileptiform discharges. He had mild dysmorphic facial features, including broad forehead, hypertelorism, downslanting palpebral fissures, ptosis, short nose, broad nasal tip, and smooth philtrum. Carr et al. (2010) concluded that FOXP1 may play a role in the development of verbal and motor skills.
Hamdan et al. (2010) identified different de novo heterozygous mutations in the FOXP1 gene (605515.0001 and 605515.0002) in 2 unrelated children of French Canadian origin with moderately impaired intellectual development, expressive language deficits, and autistic features (IDDLA; 613670). The first mutation (605515.0001) was a deletion found by array-based comparative genomic hybridization of a cohort of 80 patients with autism spectrum disorders (ASD) and 30 with intellectual disability. The second mutation (R525X; 605515.0002) was found by direct sequencing of the FOXP1 gene in a cohort of 110 patients with intellectual disability, 84 with ASD, and 51 with both. Hamdan et al. (2010) chose to examine the FOXP1 gene specifically because of the role of the FOXP2 gene (605317) in a speech and language disorder (SPCH1; 602081); patients with intellectual disability and ASD often show language impairment. The results indicated that disruption of FOXP1 has a global impact on brain development.
In a 6.5-year-old boy with impaired intellectual development and language impairment but without autistic features, Le Fevre et al. (2013) identified a de novo heterozygous intragenic deletion within the FOXP1 gene (605515.0003), predicted to result in haploinsufficiency.
In 3 unrelated children with impaired intellectual development, language impairment, and autistic features, Sollis et al. (2016) identified 3 different de novo heterozygous mutations in the FOXP1 gene (605515.0005-605515.0007). The mutations, including 1 nonsense and 2 missense, were found by whole-exome sequencing and confirmed by Sanger sequencing. In vitro studies showed that the mutations resulted in altered cellular localization and formation of protein aggregates, as well as loss of transcriptional repression activity. The variants retained the ability to interact with wildtype FOXP1, suggesting that they could exert a dominant-negative effect.
By exome sequencing, Moirangthem and Phadke (2021) identified de novo heterozygous mutations in the FOXP1 gene in 2 unrelated Indian boys with intellectual developmental disorder with language impairment. Patient 1 had an insertion/deletion mutation (c.593_599delinsAGAAG, NM_032682) resulting in a frameshift and a premature stop codon (Leu198GlufsTer7), and patient 2 had a missense mutation (c.1556T-C, NM_032682.5) resulting in a leu519-to-pro (L519P) substitution in the highly conserved FOX domain.
In a 10-year-old girl with intellectual developmental disorder with language impairment, Benvenuto et al. (2023) identified a de novo heterozygous nonsense mutation (Q344X) in exon 9 of the FOXP1 gene (c.1030C-T, NM_032682.6). The mutation was found by targeted gene panel sequencing and confirmed by Sanger sequencing. The variant was not present in the ESP6500, dbSNP, and gnomAD databases or in in-house controls and was classified as likely pathogenic by ACMG criteria.
Associations Pending Confirmation
Bekheirnia et al. (2017) performed whole-exome sequencing (WES) in 112 individuals from 62 families with a clinical diagnosis of congenital anomalies of kidney and urinary tract (CAKUT; see 610805) and identified 1 deleterious de novo SNP in the FOXP1 gene. They then queried the clinical database at the Baylor Miraca Genetic Laboratory and identified 7 additional unrelated individuals with novel de novo single-nucleotide variants (SNVs) in FOXP1. There were 3 missense mutations, 4 frameshift, and 1 splice site mutation. Functional studies were not performed. All 8 individuals had neurodevelopmental phenotypes consistent with loss of function variants in FOXP1. However, 4 of the 8 individuals also had upper urinary tract defects, and 5 had defects in the lower genitourinary tract, including undescended testis, hypospadias, and neurogenic bladder. In addition, these patients have brain and heart involvement, which is consistent with the role of FOXP1 in the development of these organs. CNS malformations, including hydrocephaly, and cardiac defects were among the phenotypes of the patients in this study.
Hu et al. (2006) found that mice lacking Foxp1 died at embryonic day 14.5 due to heart valve and outflow tract abnormalities. Reconstitution of Rag2 (179616)-deficient mice with Foxp1 -/- or Foxp1 +/- fetal liver cells resulted in decreased mature B cells, but normal thymocytes, in the recipients. Foxp1 -/- pro-B cells had reduced IgM, Rag1 (179615), and Rag2 expression, and V(D)J rearrangement was also impaired in Foxp1 -/- B cells. Chromatin immunoprecipitation and EMSA analyses showed that Foxp1 bound to Foxp site-2 (Fkh2) in the Erag enhancer, which is upstream of Rag2, in a B-lineage specific way. Hu et al. (2006) concluded that FOXP1 influences B-cell development at an early stage, and that FOXP1 deficiency results in a phenotype that resembles double haploinsufficiency of E2A (TCF3; 147141) and EBF (164343).
Feng et al. (2010) generated mice with a conditional deletion of Foxp1 in double-positive thymocytes and found that peripheral Cd4 (see 186940) and Cd8 (see 186910) cells also lacked Foxp1 and that single-positive thymocytes acquired an activated phenotype in thymus. Peripheral cells also exhibited an activated phenotype and increased apoptosis and readily produced cytokines upon T-cell receptor engagement. Feng et al. (2010) concluded that FOXP1 is an essential transcriptional regulator for thymocyte development and the generation of quiescent naive T cells.
In a French Canadian girl (patient A, R0031608) with intellectual developmental disorder with language impairment and autistic features (IDDLA; 613670), Hamdan et al. (2010) identified a de novo heterozygous 390-kb intragenic deletion in the FOXP1 gene. The deletion encompassed exons 4 to 14 of the longest FOXP1 isoform, including the translation initiation site and leucine zipper and zinc finger domains important for transcriptional activity.
In a French Canadian boy (patient B, R0024121) with intellectual developmental disorder with language impairment and autistic features (IDDLA; 613670), Hamdan et al. (2010) identified a de novo heterozygous 1573C-T transition in the FOXP1 gene, resulting in an arg525-to-ter (R525X) substitution. The mutation was predicted to abolish the last 152 residues of the protein, including part of the forkhead DNA-binding (FHD) domain and a conserved nuclear localization signal. The mutation was not found in 570 controls. In vitro functional expression studies in HEK293 cells showed that the R525X mutant impaired the transcriptional repression ability of FOXP1, consistent with a loss of function.
Sollis et al. (2016) showed that the R525X mutant protein formed large cytoplasmic aggregates and was excluded from the nuclei in cellular transfection studies; these findings suggested misfolding of the aberrant protein. The R525X variant showed a complete loss of interaction with wildtype FOXP1 and FOXP2 (605317) and was unable to self-associate, suggesting haploinsufficiency as the pathogenic mechanism.
In a 6.5-year-old boy with intellectual developmental disorder with language impairment but without autistic features (IDDLA; 613670), Le Fevre et al. (2013) identified a de novo heterozygous 190-kb intragenic deletion within the FOXP1 gene, resulting in the deletion of exons 6 to 13 and likely resulting in a truncated or nonfunctional protein, consistent with haploinsufficiency.
In a child (patient 41) with intellectual developmental disorder with language impairment (IDDLA; 613670), Srivastava et al. (2014) identified a de novo c.1600T-C transition in the FOXP1 gene, resulting in a trp534-to-arg (W534R) substitution. The patient was ascertained from a cohort of 78 patients with various neurodevelopmental disorders who underwent whole-exome sequencing. Functional studies of the FOXP1 variant were not performed, but the phenotype was consistent with previous patients who had been shown to have FOXP1 haploinsufficiency. Additional features in this patient included macrocephaly, delayed development, and delayed myelination on brain imaging.
Sollis et al. (2016) showed that the mutant W534R protein had abnormal localization and formed cytoplasmic aggregates in cellular transfection studies. Luciferase reporter assays showed that the mutant protein had significant loss of repressive activity, suggesting it would be unable to properly regulate transcription of target genes. The W534R variant showed loss of interaction with wildtype FOXP1 and FOXP2 (605317) and had a reduced ability to self-associate, consistent with haploinsufficiency as the pathogenic mechanism.
In an 11-year-old boy (patient 1) with intellectual developmental disorder with language impairment and autistic features (IDDLA; 613670), but who did not fulfill the criteria for classic autism, Sollis et al. (2016) identified a de novo heterozygous c.1393A-G transition (chr3.71,026,829A-G, GRCh37) in the FOXP1 gene, resulting in an arg465-t0-gly (R465G) substitution at a conserved residue in the DNA-binding domain. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. In vitro cellular expression studies showed that the mutant protein had abnormal localization and formed cytoplasmic and nuclear aggregates. Luciferase reporter assays showed that the mutant protein had significant loss of repressive activity, suggesting it would be unable to properly regulate transcription of target genes. The R565G variant retained the ability to interact with wildtype FOXP1 and FOXP2 (605317) and led to mislocalization of the wildtype proteins in nuclear aggregates, suggesting a possible dominant-negative effect.
In a 7-year-old Dutch boy (patient 2) with intellectual developmental disorder with language impairment and pervasive developmental disorder (IDDLA; 613670), Sollis et al. (2016) identified a de novo heterozygous c.1540C-T transition (chr3.71,021,818C-T, GRCh37) in the FOXP1 gene, resulting in an arg514-to-cys (R514C) substitution at a conserved residue in the DNA-binding domain. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. In vitro cellular expression studies showed that the mutant protein had abnormal localization and formed cytoplasmic and nuclear aggregates. Luciferase reporter assays showed that the mutant protein had a significant loss of repressive activity, suggesting it would be unable to properly regulate transcription of target genes. The R514C variant retained the ability to interact with wildtype FOXP1 and FOXP2 (605317) and led to mislocalization of the wildtype proteins in nuclear aggregates, suggesting a possible dominant-negative effect.
In a 15-year-old Dutch girl (patient 3) with intellectual developmental disorder with language impairment and pervasive developmental disorder (IDDLA; 613670), Sollis et al. (2016) identified a de novo heterozygous c.1317C-G transversion (chr3.71,027,010C-G, GRCh37) in the FOXP1 gene, resulting in a tyr439-to-ter (Y439X) substitution that truncates the protein between the leucine zipper dimerization domain and the DNA-binding domain. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. The mutation was predicted to result in FOXP1 haploinsufficiency, but no patient material was available to confirm nonsense-mediated mRNA decay of the altered transcript. In vitro studies showed that the Y439X variant formed large cytoplasmic aggregates and was absent from cell nuclei. Luciferase reporter assays showed that the mutant protein had a significant loss of repressive activity, suggesting it would be unable to properly regulate transcription of target genes. The Y439X variant retained the ability to interact with wildtype FOXP1 and FOXP2 (605317) and led to mislocalization of the wildtype proteins in cytoplasmic aggregates, suggesting a possible dominant-negative effect.
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