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HNF1B HNF1 homeobox B [ Homo sapiens (human) ]

Gene ID: 6928, updated on 8-Apr-2021

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
T2D; FJHN; HNF2; LFB3; RCAD; TCF2; HPC11; LF-B3; MODY5; TCF-2; VHNF1; ADTKD3; 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
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Genomic context

See HNF1B in Genome Data Viewer
Location:
17q12
Exon count:
11
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (37686431..37745059, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (36046434..36105050, 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 Sharpr-MPRA regulatory region 14078

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
GeneReviews: Not available
Genetic correction of PSA values using sequence variants associated with PSA levels.
GeneReviews: Not available
Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility.
GeneReviews: Not available
Genome-wide association scan for variants associated with early-onset prostate cancer.
GeneReviews: Not available
Genome-wide association study identifies a common variant associated with risk of endometrial cancer.
GeneReviews: Not available
Genome-wide association study identifies five new susceptibility loci for prostate cancer in the Japanese population.
GeneReviews: Not available
Genome-wide association study identifies new prostate cancer susceptibility loci.
GeneReviews: Not available
Genome-wide association study identifies three novel loci for type 2 diabetes.
GeneReviews: Not available
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
GeneReviews: Not available
GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.
GeneReviews: Not available
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
GeneReviews: Not available
Multiple loci identified in a genome-wide association study of prostate cancer.
GeneReviews: Not available
Multiple newly identified loci associated with prostate cancer susceptibility.
GeneReviews: Not available
Renal cell carcinoma, nonpapillary
MedGen: CN074294 OMIM: 144700 GeneReviews: Not available
Compare labs
Renal cysts and diabetes syndrome Compare labs
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
GeneReviews: Not available
Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes.
GeneReviews: Not available
Type 2 diabetes mellitus
MedGen: C0011860 OMIM: 125853 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-12-21)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-12-21)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

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 IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
circadian regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
embryonic morphogenesis IEA
Inferred from Electronic Annotation
more info
 
hepatocyte 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 
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 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 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 carbohydrate IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromatin ISA
Inferred from Sequence Alignment
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
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 

General protein information

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

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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
    5048..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, ENST00000617811.5
    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_001165923.4NP_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
    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_001304286.2NP_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 Updated Annotation Release 109.20210226

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    37686431..37745059 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.p13 ALT_REF_LOCI_1

Genomic

  1. NT_187614.1 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    1925499..1984115 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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