Developmental Brain Disorder Gene Database

LoF Variant Gene

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Tier

1

FOXP1

HGNC:3823 (protein-coding gene)

forkhead box P1

Unique Cases:
44
Disorders:
ID, ASD, EP, ADHD
Last Updated:
November 4, 2024

Summary
Cases
Publications
External

Gene Summary:

DBD Genes Classification
FOXP1 is a High Confidence candidate gene classified as Tier 1. Tier 1 genes have three or more de novo pathogenic loss-of-function variants.
Gene Function
Transcriptional repressor (PubMed:18347093, PubMed:26647308). Can act with CTBP1 to synergistically repress transcription but CTPBP1 is not essential (By similarity). Plays an important role in the specification and differentiation of lung epithelium. Acts cooperatively with FOXP4 to regulate lung secretory epithelial cell fate and regeneration by restricting the goblet cell lineage program; the function may involve regulation of AGR2. Essential transcriptional regulator of B-cell development. I... (Source: Uniprot)
Previous symbols
No previous symbols
Alias symbols
QRF1, 12CC4, HSPC215, hFKH1B
Chromosomal Location
3p13
Genomic Coordinates
GRCh37:chr3:71003865-71633140
GRCh38:chr3:70954708-71583983
Associated Disorders
Intellectual Disability, Autism, Epilepsy, Attention Deficit Hyperactivity Disorder

Predictive Scores:

HI Score (Decipher)

0.14

pLI (gnomAD)

1.00

LOEUF (gnomAD)

0.18

Classifications from External Sources:

SFARI Score (SFARI)

1

DDG2P Classification (DDG2P)

Definitive

ClinGen Classification (ClinGen)

Definitive1

Disputed1

GenCC Classification (GenCC)

Definitive3 Moderate1 Strong1 Disputed Evidence1

Publications:

Guo H et. al., Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes., Genet Med, 2019
Horn D et. al., Identification of FOXP1 deletions in three unrelated patients with mental retardation and significant speech and language deficits., Hum Mutat, 2010
Sollis E et. al., Identification and functional characterization of de novo FOXP1 variants provides novel insights into the etiology of neurodevelopmental disorder., Hum Mol Genet, 2016
Boone PM et. al., Detection of clinically relevant exonic copy-number changes by array CGH., Hum Mutat, 2010
Lee H et. al., Clinical exome sequencing for genetic identification of rare Mendelian disorders., JAMA, 2014
Iossifov I et. al., The contribution of de novo coding mutations to autism spectrum disorder., Nature, 2014
Deciphering Developmental Disorders Study. et. al., Large-scale discovery of novel genetic causes of developmental disorders., Nature, 2015
Hamdan FF et. al., De novo mutations in FOXP1 in cases with intellectual disability, autism, and language impairment., Am J Hum Genet, 2010
Girirajan S et. al., Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder., Am J Hum Genet, 2013
Guo H et. al., Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model., Mol Autism, 2018
Coe BP et. al., Refining analyses of copy number variation identifies specific genes associated with developmental delay., Nat Genet, 2014
Chérot E et. al., Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients., Clin Genet, 2018
Feliciano P et. al., Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes., NPJ Genom Med, 2019
Grozeva D et. al., Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability., Hum Mutat, 2015
Urreizti R et. al., A De Novo FOXP1 Truncating Mutation in a Patient Originally Diagnosed as C Syndrome., Sci Rep, 2018
Palumbo O et. al., 3p14.1 de novo microdeletion involving the FOXP1 gene in an adult patient with autism, severe speech delay and deficit of motor coordination., Gene, 2013
Lozano R et. al., A de novo FOXP1 variant in a patient with autism, intellectual disability and severe speech and language impairment., Eur J Hum Genet, 2015
Le Fevre AK et. al., FOXP1 mutations cause intellectual disability and a recognizable phenotype., Am J Med Genet A, 2013
Carr CW et. al., Chiari I malformation, delayed gross motor skills, severe speech delay, and epileptiform discharges in a child with FOXP1 haploinsufficiency., Eur J Hum Genet, 2010
Hua R et. al., [Clinical features and genetic analysis of three children with mental retardation, language impairment and autistic features due to de novo variants of FOXP1 gene]., Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2021
Brea-Fernández AJ et. al., Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability., Eur J Hum Genet, 2022
et. al., , ,
Miyake N et. al., Molecular diagnosis of 405 individuals with autism spectrum disorder., Eur J Hum Genet, 2023
et. al., , ,

NCBI: Gene

Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
NCBI: Gene

Gene Reviews

An international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families.
Gene Reviews

DECIPHER

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient.
DECIPHER

SFARI

SFARI Gene is an evolving online database designed to permit quick entrée into the genetics of autism, and to help researchers track the ever-expanding genetic risk factors that emerge in the literature.
SFARI

ClinGen

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.
ClinGen

GenCC

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases.
GenCC

gnomAD

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
gnomAD
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