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HNF1B HNF1 homeobox B [ Homo sapiens (human) ]

Gene ID: 6928, updated on 20-Apr-2024

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; AllianceGenome:HGNC:11630
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

Location:
17q12
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (37686431..37745059, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (38673401..38732032, complement)
105.20220307 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 microRNA 378j Neighboring gene DExD-box helicase 52 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36001021-36001522 Neighboring gene uncharacterized LOC105371756 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:36057789-36058988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36060550-36061050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36061051-36061551 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:36062200-36063399 Neighboring gene uncharacterized LOC124903989 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:36068100-36068600 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:36070779-36071300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:36071301-36071822 Neighboring gene uncharacterized LOC105371754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36083205-36083705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36090926-36091594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36091595-36092261 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:36093401-36094600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36101632-36102136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36102137-36102641 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36155829-36156606 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:36156607-36157382 Neighboring gene uncharacterized LOC105371757 Neighboring gene Sharpr-MPRA regulatory region 14078 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:36185958-36186705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36202981-36203480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:36203816-36204316 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
involved_in branching morphogenesis of an epithelial tube IEA
Inferred from Electronic Annotation
more info
 
involved_in embryonic digestive tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in endodermal cell fate specification IEA
Inferred from Electronic Annotation
more info
 
involved_in epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in hepatoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in hindbrain development IEA
Inferred from Electronic Annotation
more info
 
involved_in inner cell mass cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in insulin secretion IEA
Inferred from Electronic Annotation
more info
 
involved_in kidney development IDA
Inferred from Direct Assay
more info
PubMed 
involved_in kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in mesenchymal cell apoptotic process involved in metanephros development IEA
Inferred from Electronic Annotation
more info
 
involved_in mesonephric duct formation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of mesenchymal cell apoptotic process involved in metanephros development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in pancreas development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription initiation by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in pronephric nephron tubule development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in pronephros development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of branch elongation involved in ureteric bud branching IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of pronephros size IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in response to glucose IEA
Inferred from Electronic Annotation
more info
 
involved_in ureteric bud elongation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription regulator 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)

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
    B4DKM3, E0YMJ9, 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/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/TrEMBL
    A0A0C4DGS8, E0YMJ8
    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
  4. NM_001411100.1NP_001398029.1  hepatocyte nuclear factor 1-beta isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC243571
    Consensus CDS
    CCDS92293.1
    UniProtKB/TrEMBL
    A0A087WZC2
    Related
    ENSP00000482529.1, ENST00000614313.4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    37686431..37745059 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436630.1XP_047292586.1  hepatocyte nuclear factor 1-beta isoform X3

  2. XM_011525164.1XP_011523466.1  hepatocyte nuclear factor 1-beta isoform X1

    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
  3. XM_011525161.1XP_011523463.1  hepatocyte nuclear factor 1-beta isoform X2

    See identical proteins and their annotated locations for XP_011523463.1

    UniProtKB/TrEMBL
    E0YMJ8
    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
  4. XM_047436631.1XP_047292587.1  hepatocyte nuclear factor 1-beta isoform X5

  5. XM_011525162.3XP_011523464.1  hepatocyte nuclear factor 1-beta isoform X4

    See identical proteins and their annotated locations for XP_011523464.1

    UniProtKB/TrEMBL
    E0YMJ8
    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
  6. XM_011525163.3XP_011523465.1  hepatocyte nuclear factor 1-beta isoform X6

    See identical proteins and their annotated locations for XP_011523465.1

    UniProtKB/TrEMBL
    E0YMJ8
    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.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1925499..1984115 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329318.1XP_054185293.1  hepatocyte nuclear factor 1-beta isoform X1

  2. XM_054329319.1XP_054185294.1  hepatocyte nuclear factor 1-beta isoform X2

  3. XM_054329321.1XP_054185296.1  hepatocyte nuclear factor 1-beta isoform X5

  4. XM_054329320.1XP_054185295.1  hepatocyte nuclear factor 1-beta isoform X4

  5. XM_054329322.1XP_054185297.1  hepatocyte nuclear factor 1-beta isoform X6

  6. XM_054329323.1XP_054185298.1  hepatocyte nuclear factor 1-beta isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    38673401..38732032 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317027.1XP_054173002.1  hepatocyte nuclear factor 1-beta isoform X3

  2. XM_054317025.1XP_054173000.1  hepatocyte nuclear factor 1-beta isoform X1

  3. XM_054317026.1XP_054173001.1  hepatocyte nuclear factor 1-beta isoform X2

  4. XM_054317029.1XP_054173004.1  hepatocyte nuclear factor 1-beta isoform X5

  5. XM_054317028.1XP_054173003.1  hepatocyte nuclear factor 1-beta isoform X4

  6. XM_054317030.1XP_054173005.1  hepatocyte nuclear factor 1-beta isoform X6

  7. XM_054317031.1XP_054173006.1  hepatocyte nuclear factor 1-beta isoform X8

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.