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Hnf4a Gene Detail
Summary
  • Symbol
    Hnf4a
  • Name
    hepatic nuclear factor 4, alpha
  • Synonyms
    Hnf4, HNF-4, HNF4 alpha, MODY1, Nr2a1, Nuclear receptor 2A1, Tcf14, Tcf4
  • Feature Type
    protein coding gene
  • IDs
    MGI:109128
    NCBI Gene: 15378
  • Alliance
    genome feature page
  • Transcription Start Sites
    7 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:163348731-163414827 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 84.32 cM
  • Mapping Data
    7 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1605 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_109128
 protein coding gene Chr2:163348728-163414830 (+)
129S1/SvImJ ENSMUSG00200016359
 protein coding gene Chr2:160249715-160309357 (+)
A/J ENSMUSG00195016535
 protein coding gene Chr2:160590597-160650230 (+)
AKR/J ENSMUSG00220013642
 protein coding gene Chr2:159911488-159977555 (+)
BALB/cJ ENSMUSG00180046820
 protein coding gene Chr2:160044323-160103948 (+)
C3H/HeJ ENSMUSG00175050451
 protein coding gene Chr2:160794085-160853699 (+)
C57BL/6NJ ENSMUSG00215036205
 protein coding gene Chr2:160218563-160284680 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0024618
 protein coding gene Chr2:155352268-155412466 (+)
CAST/EiJ ENSTCUG00005043133
 protein coding gene Chr2:159150837-159217055 (+)
CBA/J ENSMUSG00210015357
 protein coding gene Chr2:160725119-160784728 (+)
DBA/2J ENSMUSG00185047683
 protein coding gene Chr2:160454814-160520890 (+)
FVB/NJ ENSMUSG00205032588
 protein coding gene Chr2:159484160-159543738 (+)
JF1/MsJ ENSUMUG00000007504
 protein coding gene Chr2:160100796-160160821 (+)
LP/J ENSMUSG00230042688
 protein coding gene Chr2:162019358-162078992 (+)
NOD/ShiLtJ ENSMUSG00190044780
 protein coding gene Chr2:160094766-160160843 (+)
NZO/HlLtJ ENSMUSG00225050461
 protein coding gene Chr2:170017181-170083258 (+)
PWK/PhJ ENSLUMG00010043690
 protein coding gene Chr2:160007420-160066864 (+)
SPRET/EiJ ENSMSPG00010027085
 protein coding gene Chr2:162778222-162836848 (+)
WSB/EiJ ENSIUOG00005039476
 protein coding gene Chr2:159849689-159909275 (+)



Homology
more
  • Human Ortholog
    HNF4A, hepatocyte nuclear factor 4 alpha
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    HNF4A, hepatocyte nuclear factor 4 alpha
  • Synonyms
    FRTS4, HNF4, HNF4a7, HNF4a8, HNF4a9, HNF4alpha, MODY, MODY1, NR2A1, NR2A21, TCF, TCF-14, TCF14
  • Links
    NCBI Gene ID: 3172
    UniProt: P41235

  • Chr Location
    20q13.12; chr20:44355699-44434596 (+)  GRCh38
Human Diseases
more
  • Diseases
    2 with Hnf4a mouse models; 5 with human HNF4A associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
 View 1 model
      
IDs
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    2 with disease annotations
  • References
    2 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    63 phenotypes from 11 alleles in 12 genetic backgrounds
    2 phenotypes from multigenic genotypes
    122 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Nullizygous embryos show delayed growth and lethality, impaired gastrulation, abnormal primitive streak and mesoderm formation, ectoderm apoptosis, and extraembryonic tissue dysplasia. Mice expressing only the alpha1 isoform show glucose intolerance whereas mice expressing alpha7 show dyslipidemia.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    124
  • GO References
    39
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    1668
  • Tissues
    422
  • cDNA Data
    93
  • Literature Summary
    213
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 15378 NCBI Gene Model | MGI Sequence Detail 66097 C57BL/6J ±  kb
    transcript NM_001312906 RefSeq | MGI Sequence Detail 4393 ZRU/MplStud  
    polypeptide P49698 UniProt | EBI | MGI Sequence Detail 474 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      9 Sequences
    • Protein Ontology
      PR:000008654 hepatocyte nuclear factor 4-alpha
      (term hierarchy)
    • InterPro Domains
      IPR049635 Hepatocyte nuclear factor 4, ligand-binding domain
      IPR049636 Hepatocyte nuclear factor 4-like, DNA-binding domain
      IPR001723 Nuclear hormone receptor
      IPR050274 Nuclear hormone receptor family NR2 subfamily
      IPR000536 Nuclear hormone receptor, ligand-binding domain
      IPR035500 Nuclear hormone receptor-like domain superfamily
      IPR000003 Retinoid X receptor/HNF4
      IPR013088 Zinc finger, NHR/GATA-type
      IPR001628 Zinc finger, nuclear hormone receptor-type
    Molecular
    Reagents
    less
    • All nucleic 141
      Genomic 10
      cDNA 96
      Primer pair 30
      Other 5
      Antibodies 19

      Microarray probesets 7
    Other
    Accession IDs
    less
    MGD-MRK-38172
    References
    more
    • Summaries
      All 477
      Developmental Gene Expression 213
      Diseases 2
      Gene Ontology 39
      Phenotypes 122
    • Earliest
      J:912 Avraham KB, et al., Murine chromosomal location of four hepatocyte-enriched transcription factors: HNF-3 alpha, HNF-3 beta, HNF-3 gamma, and HNF-4. Genomics. 1992 Jun;13(2):264-8
    • Latest
      J:390615 Yang L, et al., PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration. Nat Commun. 2026 Jun 12;17(1)
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory