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    HNF4A hepatocyte nuclear factor 4, alpha [ Homo sapiens (human) ]

    Gene ID: 3172, updated on 30-Jun-2015
    Official Symbol
    HNF4Aprovided by HGNC
    Official Full Name
    hepatocyte nuclear factor 4, alphaprovided by HGNC
    Primary source
    HGNC:HGNC:5024
    See related
    Ensembl:ENSG00000101076; HPRD:02612; MIM:600281; Vega:OTTHUMG00000032531
    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
    TCF; HNF4; MODY; FRTS4; MODY1; NR2A1; TCF14; HNF4a7; HNF4a8; HNF4a9; NR2A21; HNF4alpha
    Summary
    The protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines. Mutations in this gene have been associated with monogenic autosomal dominant non-insulin-dependent diabetes mellitus type I. Alternative splicing of this gene results in multiple transcript variants encoding several different isoforms. [provided by RefSeq, Apr 2012]
    Orthologs
    See HNF4A in Epigenomics, MapViewer
    Location:
    20q13.12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 20 NC_000020.11 (44355801..44432845)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42984441..43061485)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene fat storage-inducing transmembrane protein 2 Neighboring gene uncharacterized LOC105372629 Neighboring gene R3H domain containing-like Neighboring gene HNF4A antisense RNA 1 Neighboring gene microRNA 3646 Neighboring gene long intergenic non-protein coding RNA 1430 Neighboring gene chromosome 20 open reading frame 62

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Diabetes mellitus type 2
    MedGen: C0011860 OMIM: 125853 GeneReviews: Not available
    Compare labs
    familial hyperinsulinism
    MedGen: CN043604 GeneReviews: Familial Hyperinsulinism
    Compare labs
    Fanconi renotubular syndrome 4 with maturity-onset diabetes of the young
    MedGen: CN219570 OMIM: 616026 GeneReviews: Not available
    not available
    Maturity-onset diabetes of the young, type 1
    MedGen: C1852093 OMIM: 125850 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    NHGRI GWA Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    NHGRI GWA Catalog
    Discovery and refinement of loci associated with lipid levels.
    NHGRI GWA Catalog
    Genome-wide association and population genetic analysis of C-reactive protein in African American and Hispanic American women.
    NHGRI GWA Catalog
    Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.
    NHGRI GWA Catalog
    Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
    NHGRI GWA Catalog
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    NHGRI GWA Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Clone Names

    • FLJ39654

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    SMAD protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    blood coagulation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endocrine pancreas development TAS
    Traceable Author Statement
    more info
     
    gene expression TAS
    Traceable Author Statement
    more info
     
    glucose homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    intracellular receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    lipid homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ornithine metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    phospholipid homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of cholesterol homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of gastrulation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of growth hormone receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    regulation of insulin secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of lipid metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to glucose ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sex differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    signal transduction involved in regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    steroid hormone mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    transcription initiation from RNA polymerase II promoter TAS
    Traceable Author Statement
    more info
     
    triglyceride homeostasis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    xenobiotic metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    hepatocyte nuclear factor 4-alpha
    Names
    HNF4alpha10/11/12
    TCF-14
    hepatic nuclear factor 4 alpha
    nuclear receptor subfamily 2 group A member 1
    transcription factor 14
    transcription factor HNF-4

    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_009818.1 RefSeqGene

      Range
      5001..82045
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_483

    mRNA and Protein(s)

    1. NM_000457.4NP_000448.3  hepatocyte nuclear factor 4-alpha isoform HNF4alpha2

      See identical proteins and their annotated locations for NP_000448.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (HNF4alpha2).
      Source sequence(s)
      AL132772, AW134564, BP274413, HQ692869
      Consensus CDS
      CCDS13330.1
      UniProtKB/TrEMBL
      F1D8T1
      UniProtKB/Swiss-Prot
      P41235
      Conserved Domains (2) summary
      cd06931
      Location:151373
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:60135
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    2. NM_001030003.2NP_001025174.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha7

      See identical proteins and their annotated locations for NP_001025174.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' terminal exon (resulting in translation initiation from an alternate upstream start codon) and uses an alternate in-frame donor splice site in the 3' coding region compared to variant 2. The resulting shorter isoform (HNF4alpha7) has a distinct N-terminus and lacks a 10 aa protein segment in the C-terminal region compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AW134564, AY680696
      Consensus CDS
      CCDS46604.1
      UniProtKB/Swiss-Prot
      P41235
      Conserved Domains (2) summary
      cd06931
      Location:129351
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:38113
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    3. NM_001030004.2NP_001025175.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha9

      See identical proteins and their annotated locations for NP_001025175.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate 5' terminal exon (resulting in translation initiation from an alternate upstream start codon) and differs at the 3' end that causes a frame-shift compared to variant 2. The resulting shorter isoform (HNF4alpha9) has distinct N- and C-termini compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AY680698
      Consensus CDS
      CCDS68131.1
      UniProtKB/Swiss-Prot
      P41235
      Related
      ENSP00000476609, OTTHUMP00000274118, ENST00000609795, OTTHUMT00000472003
      Conserved Domains (2) summary
      cd06931
      Location:129351
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:38113
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    4. NM_001258355.1NP_001245284.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha4

      See identical proteins and their annotated locations for NP_001245284.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) contains an additional coding exon in the 5' region that results in translation initiation from an alternate downstream start codon compared to variant 2. The resulting shorter isoform (HNF4alpha4) has a distinct N-terminus compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AW134564, BP274413, HQ692869, Z49825
      UniProtKB/TrEMBL
      F1D8T1
      UniProtKB/Swiss-Prot
      P41235
      Conserved Domains (2) summary
      cd06931
      Location:144366
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:53128
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    5. NM_001287182.1NP_001274111.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha10

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs at the 5' end (resulting in translation initiation from an alternate upstream start codon) and uses an alternate in-frame donor splice site in the 3' coding region compared to variant 2. The resulting shorter isoform (HNF4alpha10) has a distinct N-terminus and lacks a 10 aa protein segment in the C-terminal region compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AW134564, AY680696, FJ608822
      UniProtKB/TrEMBL
      B9VVT8
      UniProtKB/Swiss-Prot
      P41235
      Conserved Domains (2) summary
      cd06931
      Location:126348
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:35110
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    6. NM_001287183.1NP_001274112.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha11

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs at the 5' end, which results in translation initiation from an alternate upstream start codon compared to variant 2. The resulting shorter isoform (HNF4alpha11) has a distinct N-terminus compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AW134564, AY680697, FJ608822
      Consensus CDS
      CCDS74728.1
      UniProtKB/TrEMBL
      A0A087WXV4
      UniProtKB/TrEMBL
      B9VVT8
      UniProtKB/Swiss-Prot
      P41235
      Related
      ENSP00000481331, ENST00000619550
      Conserved Domains (2) summary
      cd06931
      Location:126348
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:35110
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    7. NM_001287184.1NP_001274113.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha12

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) differs at the 5' end (resulting in translation initiation from an alternate upstream start codon) and at the 3' end (that causes a frame-shift) compared to variant 2. The resulting shorter isoform (HNF4alpha12) has distinct N- and C-termini compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AY680698, BC137539, FJ608822
      UniProtKB/TrEMBL
      B9VVT8
      UniProtKB/Swiss-Prot
      P41235
      Conserved Domains (2) summary
      cd06931
      Location:126348
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:35110
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    8. NM_175914.4NP_787110.2  hepatocyte nuclear factor 4-alpha isoform HNF4alpha8

      See identical proteins and their annotated locations for NP_787110.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate 5' terminal exon, which results in translation initiation from an alternate upstream start codon compared to variant 2. The resulting shorter isoform (HNF4alpha8) has a distinct N-terminus compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AW134564, AY680697
      Consensus CDS
      CCDS42876.1
      UniProtKB/TrEMBL
      F1D8T0
      UniProtKB/Swiss-Prot
      P41235
      Conserved Domains (2) summary
      cd06931
      Location:129351
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:38113
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    9. NM_178849.2NP_849180.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha1

      See identical proteins and their annotated locations for NP_849180.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame donor splice site in the 3' coding region compared to variant 2. The resulting shorter isoform (HNF4alpha1) lacks a 10 aa protein segment compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, AW134564, BP274413, HQ692860
      Consensus CDS
      CCDS46605.1
      UniProtKB/TrEMBL
      F1D8S2
      Conserved Domains (2) summary
      cd06931
      Location:151373
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:60135
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    10. NM_178850.2NP_849181.1  hepatocyte nuclear factor 4-alpha isoform HNF4alpha3

      See identical proteins and their annotated locations for NP_849181.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has a different 3' end that causes a frame-shift compared to variant 2. The resulting shorter isoform (HNF4alpha3) has a distinct C-terminus compared to isoform HNF4alpha2.
      Source sequence(s)
      AL132772, BC137539, BP274413
      Consensus CDS
      CCDS13331.1
      UniProtKB/Swiss-Prot
      P41235
      Related
      ENSP00000410911, OTTHUMP00000031062, ENST00000443598, OTTHUMT00000079365
      Conserved Domains (2) summary
      cd06931
      Location:151373
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:60135
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p2 Primary Assembly

      Range
      44355801..44432845
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005260407.2XP_005260464.1  

      Conserved Domains (2) summary
      cd06931
      Location:190412
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:99174
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    2. XM_011528798.1XP_011527100.1  

      Conserved Domains (2) summary
      cd06931
      Location:167389
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:76151
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers
    3. XM_011528797.1XP_011527099.1  

      Conserved Domains (2) summary
      cd06931
      Location:167389
      NR_LBD_HNF4_like; The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes
      cd06960
      Location:76151
      NR_DBD_HNF4A; DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

    Alternate CHM1_1.1

    Genomic

    1. NC_018931.2 Alternate CHM1_1.1

      Range
      42886684..42964390
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)