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HNF1A HNF1 homeobox A [ Homo sapiens (human) ]

Gene ID: 6927, updated on 8-Jul-2018
Official Symbol
HNF1Aprovided by HGNC
Official Full Name
HNF1 homeobox Aprovided by HGNC
Primary source
HGNC:HGNC:11621
See related
Ensembl:ENSG00000135100 MIM:142410; Vega:OTTHUMG00000151015
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
HNF1; LFB1; TCF1; HNF4A; MODY3; TCF-1; HNF-1A; IDDM20
Summary
The protein encoded by this gene is a transcription factor required for the expression of several liver-specific genes. The encoded protein functions as a homodimer and binds to the inverted palindrome 5'-GTTAATNATTAAC-3'. Defects in this gene are a cause of maturity onset diabetes of the young type 3 (MODY3) and also can result in the appearance of hepatic adenomas. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]
Expression
Biased expression in kidney (RPKM 13.4), duodenum (RPKM 9.8) and 6 other tissues See more
Orthologs
See HNF1A in Genome Data Viewer
Location:
12q24.31
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (120977683..121002512)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (121415861..121440315)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L12 pseudogene 33 Neighboring gene HNF1A antisense RNA 1 Neighboring gene chromosome 12 open reading frame 43 Neighboring gene 2'-5'-oligoadenylate synthetase like Neighboring gene uncharacterized LOC105378258

  • Project title: 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Diabetes mellitus type 1
MedGen: C0011854 OMIM: 222100 GeneReviews: Not available
Compare labs
Diabetes mellitus type 2
MedGen: C0011860 OMIM: 125853 GeneReviews: Not available
not available
Diabetes mellitus, insulin-dependent, 20
MedGen: C2675866 OMIM: 612520 GeneReviews: Not available
Compare labs
Hepatic adenomas, familial
MedGen: C1840646 OMIM: 142330 GeneReviews: Not available
Compare labs
Maturity-onset diabetes of the young, type 3 Compare labs
Renal cell carcinoma, nonpapillary
MedGen: C3160732 OMIM: 144700 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Are C-reactive protein associated genetic variants associated with serum levels and retinal markers of microvascular pathology in Asian populations from Singapore?
NHGRI GWA Catalog
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
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
Genetic associations with C-reactive protein level and white blood cell count in the KARE study.
NHGRI GWA Catalog
Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease.
NHGRI GWA Catalog
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
NHGRI GWA Catalog
Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.
NHGRI GWA Catalog
Genome-wide association analysis of blood biomarkers in chronic obstructive pulmonary disease.
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 for C-reactive protein levels identified pleiotropic associations in the IL6 locus.
NHGRI GWA Catalog
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
NHGRI GWA Catalog
Genome-wide association study of type 2 diabetes in a sample from Mexico City and a meta-analysis of a Mexican-American sample from Starr County, Texas.
NHGRI GWA Catalog
Genome-wide association with C-reactive protein levels in CLHNS: evidence for the CRP and HNF1A loci and their interaction with exposure to a pathogenic environment.
NHGRI GWA Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
NHGRI GWA Catalog
Genomics meets glycomics-the first GWAS study of human N-Glycome identifies HNF1α as a master regulator of plasma protein fucosylation.
NHGRI GWA Catalog
Joint influence of small-effect genetic variants on human longevity.
NHGRI GWA Catalog
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
NHGRI GWA Catalog
Loci affecting gamma-glutamyl transferase in adults and adolescents show age × SNP interaction and cardiometabolic disease associations.
NHGRI GWA Catalog
Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study.
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
New susceptibility locus for coronary artery disease on chromosome 3q22.3.
NHGRI GWA Catalog
New variants including ARG1 polymorphisms associated with C-reactive protein levels identified by genome-wide association and pathway analysis.
NHGRI GWA Catalog
Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein.
NHGRI GWA Catalog
Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.
NHGRI GWA Catalog
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
NHGRI GWA Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
glucose homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
glucose import IMP
Inferred from Mutant Phenotype
more info
PubMed 
natural killer cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription initiation from RNA polymerase II promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
NOT regulation of pronephros size IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
renal glucose absorption IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
hepatocyte nuclear factor 1-alpha
Names
HNF-1-alpha
albumin proximal factor
hepatic nuclear factor 1
interferon production regulator factor
liver-specific transcription factor LF-B1
transcription factor 1, hepatic
truncated hepatocyte nuclear factor 1 alpha

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_011731.2 RefSeqGene

    Range
    4823..28767
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_522

mRNA and Protein(s)

  1. NM_000545.6NP_000536.5  hepatocyte nuclear factor 1-alpha isoform 2

    See identical proteins and their annotated locations for NP_000536.5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC079602, BC104908, HM116541, HM449088, M57732, X71346
    Consensus CDS
    CCDS9209.1
    UniProtKB/Swiss-Prot
    P20823
    UniProtKB/TrEMBL
    E0YMI7
    Related
    ENSP00000257555.4, OTTHUMP00000198944, ENST00000257555.10, OTTHUMT00000320957
    Conserved Domains (4) summary
    cd00086
    Location:200273
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam04812
    Location:282540
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04813
    Location:542630
    HNF-1A_C; Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus
    pfam04814
    Location:8167
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  2. NM_001306179.1NP_001293108.1  hepatocyte nuclear factor 1-alpha isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC079602, BC143483, HM116541, HM449088, X71346
    Consensus CDS
    CCDS76611.1
    UniProtKB/Swiss-Prot
    P20823
    UniProtKB/TrEMBL
    E0YMI7
    Related
    ENSP00000438804.1, OTTHUMP00000240206, ENST00000544413.2, OTTHUMT00000402514
    Conserved Domains (4) summary
    cd00086
    Location:200273
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam04812
    Location:282540
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04813
    Location:549637
    HNF-1A_C; Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus
    pfam04814
    Location:8167
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    120977683..121002512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024449168.1XP_024304936.1  hepatocyte nuclear factor 1-alpha isoform X1

    Related
    ENSP00000443112.1, ENST00000541395.5
    Conserved Domains (4) summary
    cd00086
    Location:200273
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam04813
    Location:573661
    HNF-1A_C; Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus
    pfam04812
    Location:282540
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8167
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
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