FOXA2 forkhead box A2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FOXA2provided by HGNC
Official Full Name: forkhead box A2provided by HGNC
Primary source: HGNC:HGNC:5022
See related: Ensembl:ENSG00000125798 MIM:600288; AllianceGenome:HGNC:5022
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: HNF3B; TCF3B; HNF-3-beta
Summary: This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific genes such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. This gene has been linked to sporadic cases of maturity-onset diabetes of the young. Transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]
Expression: Biased expression in stomach (RPKM 15.2), lung (RPKM 9.0) and 8 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20p11.21

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (22580998..22585490, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (22640367..22644859, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (22561636..22566128, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

FOXA2 rewires AP-1 for transcriptional reprogramming and lineage plasticity in prostate cancer.
Title: FOXA2 rewires AP-1 for transcriptional reprogramming and lineage plasticity in prostate cancer.
Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the loss of FOXA2 or its regulatory elements.
Title: Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the loss of FOXA2 or its regulatory elements.
Analysis of GATA3 and FOXA2 expression suggests that downregulation of genes involved in the maintenance of a mature yolk sac tumor phenotype may underlie sarcomatoid transformation.
Title: Analysis of GATA3 and FOXA2 expression suggests that downregulation of genes involved in the maintenance of a mature yolk sac tumor phenotype may underlie sarcomatoid transformation.
FOXA2-initiated transcriptional activation of INHBA induced by methylmalonic acid promotes pancreatic neuroendocrine neoplasm progression.
Title: FOXA2-initiated transcriptional activation of INHBA induced by methylmalonic acid promotes pancreatic neuroendocrine neoplasm progression.
Uncovering the role of FOXA2 in the Development of Human Serotonin Neurons.
Title: Uncovering the role of FOXA2 in the Development of Human Serotonin Neurons.
FOXA2 activates HIF2alpha expression to promote tumor progression and is regulated by the E3 ubiquitin ligase VHL in renal cell carcinoma.
Title: FOXA2 activates HIF2α expression to promote tumor progression and is regulated by the E3 ubiquitin ligase VHL in renal cell carcinoma.
FOXA2 suppresses gallbladder carcinoma cell migration, invasion, and epithelial-mesenchymal transition by targeting SERPINB5.
Title: FOXA2 suppresses gallbladder carcinoma cell migration, invasion, and epithelial-mesenchymal transition by targeting SERPINB5.
FOXA2 Suppression by TRIM36 Exerts Anti-Tumor Role in Colorectal Cancer Via Inducing NRF2/GPX4-Regulated Ferroptosis.
Title: FOXA2 Suppression by TRIM36 Exerts Anti-Tumor Role in Colorectal Cancer Via Inducing NRF2/GPX4-Regulated Ferroptosis.
SENP1 knockdown-mediated CTCF SUMOylation enhanced its stability and alleviated lipopolysaccharide-evoked inflammatory injury in human lung fibroblasts via regulation of FOXA2 transcription.
Title: SENP1 knockdown-mediated CTCF SUMOylation enhanced its stability and alleviated lipopolysaccharide-evoked inflammatory injury in human lung fibroblasts via regulation of FOXA2 transcription.
Hepatocyte-specific HDAC3 ablation promotes hepatocellular carcinoma in females by suppressing Foxa1/2.
Title: Hepatocyte-specific HDAC3 ablation promotes hepatocellular carcinoma in females by suppressing Foxa1/2.

Submit: New GeneRIF Correction See all GeneRIFs (164)

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

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance. EBI GWAS Catalog EBI GWAS CatalogPubMed
A weighted false discovery rate control procedure reveals alleles at FOXA2 that influence fasting glucose levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians. EBI GWAS Catalog EBI GWAS CatalogPubMed
Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48123 (e-PCR)
- UniSTS:79250

Foxa2 (e-PCR), detects polymorphism
- UniSTS:464791

G59567 (e-PCR)
- UniSTS:136871

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	IBA Inferred from Biological aspect of Ancestor more info
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	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	EXP Inferred from Experiment more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in adult locomotory behavior	ISS Inferred from Sequence or Structural Similarity more info
involved_in anatomical structure morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell fate specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in dopaminergic neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in dopaminergic neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in dopaminergic neuron differentiation	TAS Traceable Author Statement more info	PubMed
involved_in endocrine pancreas development	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of epithelial to mesenchymal transition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell-cell adhesion mediated by cadherin	IC Inferred by Curator more info	PubMed
involved_in positive regulation of embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gastrulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed
involved_in primitive streak formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of blood coagulation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of insulin secretion involved in cellular response to glucose stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in response to interleukin-6	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell junction	IDA Inferred from Direct Assay more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: hepatocyte nuclear factor 3-beta

Names: forkhead box protein A2; hepatic nuclear factor-3-beta; transcription factor 3B

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.

mRNA and Protein(s)

NM_021784.5 → NP_068556.2 hepatocyte nuclear factor 3-beta isoform 1

See identical proteins and their annotated locations for NP_068556.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AL121722

Consensus CDS

CCDS46585.1

UniProtKB/TrEMBL

B0ZTD4

Related

ENSP00000400341.3, ENST00000419308.7

Conserved Domains (3) summary

pfam08430
Location:23 → 164

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:380 → 452

HNF_C; HNF3 C-terminal domain

cd20039
Location:163 → 264

FH_FOXA2; Forkhead (FH) domain found in Forkhead box protein A2 (FOXA2) and similar proteins
NM_153675.3 → NP_710141.1 hepatocyte nuclear factor 3-beta isoform 2

See identical proteins and their annotated locations for NP_710141.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has a different splice pattern at the 5' end compared to transcript variant 1, resulting in translation initiation from a downstream AUG, and a shorter isoform (2) missing 6 aa from the N-terminus compared to isoform 1.

Source sequence(s)

AA469087, AB028021, AI268650, AL121722

Consensus CDS

CCDS13147.1

UniProtKB/Swiss-Prot

Q8WUW4, Q96DF7, Q9Y261

Related

ENSP00000366319.4, ENST00000377115.4

Conserved Domains (3) summary

pfam08430
Location:17 → 158

Forkhead_N; Forkhead N-terminal region

pfam09354
Location:374 → 446

HNF_C; HNF3 C-terminal domain

cd20039
Location:157 → 258

FH_FOXA2; Forkhead (FH) domain found in Forkhead box protein A2 (FOXA2) and similar proteins

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

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

22580998..22585490 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047440133.1 → XP_047296089.1 hepatocyte nuclear factor 3-beta isoform X1

UniProtKB/Swiss-Prot

Q8WUW4, Q96DF7, Q9Y261
XM_047440134.1 → XP_047296090.1 hepatocyte nuclear factor 3-beta isoform X2