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HNF1B HNF1 homeobox B [ Homo sapiens (human) ]

Gene ID: 6928, updated on 7-Dec-2018

Summary

Official Symbol
HNF1Bprovided by HGNC
Official Full Name
HNF1 homeobox Bprovided by HGNC
Primary source
HGNC:HGNC:11630
See related
Ensembl:ENSG00000275410 MIM:189907
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
FJHN; HNF2; LFB3; TCF2; HPC11; LF-B3; MODY5; TCF-2; VHNF1; HNF-1B; HNF1beta; HNF-1-beta
Summary
This gene encodes a member of the homeodomain-containing superfamily of transcription factors. The protein binds to DNA as either a homodimer, or a heterodimer with the related protein hepatocyte nuclear factor 1-alpha. The gene has been shown to function in nephron development, and regulates development of the embryonic pancreas. Mutations in this gene result in renal cysts and diabetes syndrome and noninsulin-dependent diabetes mellitus, and expression of this gene is altered in some types of cancer. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
Expression
Biased expression in kidney (RPKM 16.9), gall bladder (RPKM 7.3) and 11 other tissues See more
Orthologs

Genomic context

See HNF1B in Genome Data Viewer
Location:
17q12
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (37686431..37745078, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (36046434..36105096, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371755 Neighboring gene microRNA 378j Neighboring gene DExD-box helicase 52 Neighboring gene uncharacterized LOC105371756 Neighboring gene uncharacterized LOC107985009 Neighboring gene uncharacterized LOC105371754 Neighboring gene uncharacterized LOC105371757 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon pseudogene 7

Genomic regions, transcripts, and products

Expression

  • 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

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Diabetes mellitus type 2
MedGen: C0011860 OMIM: 125853 GeneReviews: Not available
not available
Familial hypoplastic, glomerulocystic kidney Compare labs
Renal cell carcinoma, nonpapillary
MedGen: C3160732 OMIM: 144700 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-19)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-19)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
NHGRI GWA Catalog
Genetic correction of PSA values using sequence variants associated with PSA levels.
NHGRI GWA Catalog
Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility.
NHGRI GWA Catalog
Genome-wide association scan for variants associated with early-onset prostate cancer.
NHGRI GWA Catalog
Genome-wide association study identifies a common variant associated with risk of endometrial cancer.
NHGRI GWA Catalog
Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.
NHGRI GWA Catalog
Genome-wide association study identifies new prostate cancer susceptibility loci.
NHGRI GWA Catalog
Genome-wide association study identifies three novel loci for type 2 diabetes.
NHGRI GWA Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
NHGRI GWA Catalog
GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.
NHGRI GWA Catalog
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
NHGRI GWA Catalog
Multiple loci identified in a genome-wide association study of prostate cancer.
NHGRI GWA Catalog
Multiple newly identified loci associated with prostate cancer susceptibility.
NHGRI GWA Catalog
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
NHGRI GWA Catalog
Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes.
NHGRI GWA Catalog

Pathways from BioSystems

  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Maturity onset diabetes of the young, organism-specific biosystem (from KEGG)
    Maturity onset diabetes of the young, organism-specific biosystemAbout 2-5% of type II diabetic patients suffer from a monogenic disease with autosomal dominant inheritance. This monogenic form of type II diabetes is called maturity onset diabetes of the young (MO...
  • Maturity onset diabetes of the young, conserved biosystem (from KEGG)
    Maturity onset diabetes of the young, conserved biosystemAbout 2-5% of type II diabetic patients suffer from a monogenic disease with autosomal dominant inheritance. This monogenic form of type II diabetes is called maturity onset diabetes of the young (MO...
  • Regulation of beta-cell development, organism-specific biosystem (from REACTOME)
    Regulation of beta-cell development, organism-specific biosystemThe normal development of the pancreas during gestation has been intensively investigated over the past decade especially in the mouse (Servitja and Ferrer 2004; Chakrabarti and Mirmira 2003). Studie...
  • Regulation of gene expression in early pancreatic precursor cells, organism-specific biosystem (from REACTOME)
    Regulation of gene expression in early pancreatic precursor cells, organism-specific biosystemThe properties of transcriptional networks early in the differentiation of human pancreatic cells are inferred from the properties of well-studied networks in mouse models. In mice, the first visible...
  • Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, organism-specific biosystem (from REACTOME)
    Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells, organism-specific biosystemThe properties of transcriptional networks in late stage (branching morphogenesis) pancreatic bud precursor cells are inferred from the properties of well-studied networks in mouse models. In mice, c...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
branching morphogenesis of an epithelial tube IEA
Inferred from Electronic Annotation
more info
 
circadian regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
embryonic digestive tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
endodermal cell fate specification IEA
Inferred from Electronic Annotation
more info
 
epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
hepatoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
hepatocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
hindbrain development IEA
Inferred from Electronic Annotation
more info
 
inner cell mass cell differentiation IEA
Inferred from Electronic Annotation
more info
 
insulin secretion IEA
Inferred from Electronic Annotation
more info
 
kidney development IDA
Inferred from Direct Assay
more info
PubMed 
kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
mesonephric duct formation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of mesenchymal cell apoptotic process involved in metanephros development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
pancreas development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription initiation from RNA polymerase II promoter IDA
Inferred from Direct Assay
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 
pronephric nephron tubule development IGI
Inferred from Genetic Interaction
more info
PubMed 
pronephros development IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein-DNA complex assembly IEA
Inferred from Electronic Annotation
more info
 
regulation of Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
regulation of branch elongation involved in ureteric bud branching IEA
Inferred from Electronic Annotation
more info
 
regulation of endodermal cell fate specification IEA
Inferred from Electronic Annotation
more info
 
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 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to glucose IEA
Inferred from Electronic Annotation
more info
 
response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
 
ureteric bud elongation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
hepatocyte nuclear factor 1-beta
Names
HNF1 beta A
homeoprotein LFB3
transcription factor 2, hepatic

NCBI Reference Sequences (RefSeq)

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_013019.2 RefSeqGene

    Range
    5029..63676
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000458.4NP_000449.1  hepatocyte nuclear factor 1-beta isoform 1

    See identical proteins and their annotated locations for NP_000449.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC017714
    Consensus CDS
    CCDS11324.1
    UniProtKB/Swiss-Prot
    P35680
    UniProtKB/TrEMBL
    Q6FHW6
    Related
    ENSP00000480291.1, ENST00000617811.4
    Conserved Domains (3) summary
    cd00086
    Location:232305
    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:314550
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  2. NM_001165923.3NP_001159395.1  hepatocyte nuclear factor 1-beta isoform 2

    See identical proteins and their annotated locations for NP_001159395.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AK296633, BC017714, X58840
    Consensus CDS
    CCDS58538.1
    UniProtKB/Swiss-Prot
    P35680
    UniProtKB/TrEMBL
    E0YMJ6
    Related
    ENSP00000482711.1, ENST00000621123.4
    Conserved Domains (3) summary
    cd00086
    Location:206279
    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:288524
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  3. NM_001304286.1NP_001291215.1  hepatocyte nuclear factor 1-beta isoform 3

    See identical proteins and their annotated locations for NP_001291215.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR, uses an alternate in-frame splice site in the central coding region, and lacks two alternate exons in the 3' coding region, resulting in a frameshift compared to variant 1. The resulting isoform (3) is shorter, and contains a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC017714, HM116556, X58840
    Consensus CDS
    CCDS77007.1
    UniProtKB/Swiss-Prot
    P35680
    UniProtKB/TrEMBL
    A0A0C4DGS8
    Related
    ENSP00000477524.1, ENST00000613727.4
    Conserved Domains (3) summary
    cd00086
    Location:206279
    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:288426
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    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_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    37686431..37745078 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525164.1XP_011523466.1  hepatocyte nuclear factor 1-beta isoform X5

    See identical proteins and their annotated locations for XP_011523466.1

    Conserved Domains (3) summary
    cd00086
    Location:206279
    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:288488
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  2. XM_011525161.1XP_011523463.1  hepatocyte nuclear factor 1-beta isoform X2

    See identical proteins and their annotated locations for XP_011523463.1

    Conserved Domains (3) summary
    cd00086
    Location:232305
    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:314485
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  3. XM_011525160.1XP_011523462.1  hepatocyte nuclear factor 1-beta isoform X1

    See identical proteins and their annotated locations for XP_011523462.1

    UniProtKB/TrEMBL
    A0A087WZC2
    Related
    ENSP00000482529.1, ENST00000614313.4
    Conserved Domains (3) summary
    cd00086
    Location:232305
    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:314514
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  4. XM_011525162.2XP_011523464.1  hepatocyte nuclear factor 1-beta isoform X3

    See identical proteins and their annotated locations for XP_011523464.1

    Conserved Domains (3) summary
    cd00086
    Location:232305
    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:314363
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus
  5. XM_011525163.2XP_011523465.1  hepatocyte nuclear factor 1-beta isoform X4

    See identical proteins and their annotated locations for XP_011523465.1

    Conserved Domains (3) summary
    cd00086
    Location:232305
    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:314349
    HNF-1B_C; Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus
    pfam04814
    Location:8173
    HNF-1_N; Hepatocyte nuclear factor 1 (HNF-1), N terminus

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NT_187614.1 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    1925499..1984134 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_006481.1: Suppressed sequence

    Description
    NM_006481.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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