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Aliases for HNF1A Gene

Aliases for HNF1A Gene

  • HNF1 Homeobox A 2 3 5
  • Liver-Specific Transcription Factor LF-B1 3 4
  • HNF-1-Alpha 3 4
  • HNF-1A 3 4
  • TCF-1 3 4
  • TCF1 3 4
  • LFB1 3 4
  • Transcription Factor 1, Hepatic; LF-B1, Hepatic Nuclear Factor (HNF1), Albumin Proximal Factor 2
  • Truncated Hepatocyte Nuclear Factor 1 Alpha 3
  • Interferon Production Regulator Factor 3
  • Hepatocyte Nuclear Factor 1-Alpha 3
  • Transcription Factor 1, Hepatic 3
  • Hepatic Nuclear Factor 1 3
  • Albumin Proximal Factor 3
  • Transcription Factor 1 4
  • IDDM20 3
  • HNF4A 3
  • MODY3 3
  • HNF1 3

External Ids for HNF1A Gene

Previous HGNC Symbols for HNF1A Gene

  • MODY3
  • TCF1

Previous GeneCards Identifiers for HNF1A Gene

  • GC12P119900
  • GC12P121416
  • GC12P118425

Summaries for HNF1A Gene

Entrez Gene Summary for HNF1A Gene

  • 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]

GeneCards Summary for HNF1A Gene

HNF1A (HNF1 Homeobox A) is a Protein Coding gene. Diseases associated with HNF1A include Maturity-Onset Diabetes Of The Young, Type 3 and Diabetes Mellitus, Insulin-Dependent, 20. Among its related pathways are ERK Signaling and Adipogenesis. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is HNF1B.

UniProtKB/Swiss-Prot for HNF1A Gene

  • Transcriptional activator that regulates the tissue specific expression of multiple genes, especially in pancreatic islet cells and in liver. Required for the expression of several liver specific genes. Binds to the inverted palindrome 5-GTTAATNATTAAC-3.

Gene Wiki entry for HNF1A Gene

Additional gene information for HNF1A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HNF1A Gene

Genomics for HNF1A Gene

GeneHancer (GH) Regulatory Elements for HNF1A Gene

Promoters and enhancers for HNF1A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J120977 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 650.7 +3.4 3408 8.2 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 ETS1 YY1 SLC30A9 ZNF121 HNF1A HNF1A-AS1 PSMD9 PXN GCN1 SETD1B RPLP0 MLEC SPPL3 C12orf43
GH12J120976 Enhancer 0.3 dbSUPER 650.7 -1.4 -1362 0.7 SSRP1 HNF1A C12orf43 COQ5 HNF1A-AS1 RPL12P33
GH12J120971 Enhancer 1.2 Ensembl ENCODE dbSUPER 0.7 -4.9 -4917 3.4 HDAC1 FOXA2 BMI1 RAD21 RFX5 YY1 ZNF335 ZNF366 ZNF143 RCOR1 C12orf43 ACADS SPPL3 HNF1A HNF1A-AS1 RPL12P33
GH12J120958 Enhancer 1.3 Ensembl ENCODE dbSUPER 0.4 -16.7 -16713 5.5 PKNOX1 BATF IRF4 RARA ATF7 IKZF2 RUNX3 CREM PAF1 SP5 ACADS C12orf43 SPPL3 OASL ENSG00000256569 ENSG00000255946 UNC119B MLEC ENSG00000256364 P2RX4
GH12J120964 Enhancer 0.2 FANTOM5 2.1 -12.8 -12800 0 OASL UNC119B ENSG00000256364 P2RX4 MSI1 RPS27P25 HNF1A HNF1A-AS1 RPL12P33
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HNF1A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HNF1A gene promoter:
  • p53
  • YY1
  • Sp1
  • NF-kappaB1
  • NF-kappaB
  • C/EBPalpha
  • HNF-1
  • HNF-1A

Genomic Locations for HNF1A Gene

Genomic Locations for HNF1A Gene
24,726 bases
Plus strand
23,970 bases
Plus strand

Genomic View for HNF1A Gene

Genes around HNF1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HNF1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HNF1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HNF1A Gene

Proteins for HNF1A Gene

  • Protein details for HNF1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hepatocyte nuclear factor 1-alpha
    Protein Accession:
    Secondary Accessions:
    • A5Z2R8
    • E0YMJ5
    • E0YMK0
    • E0YMK1
    • E2I9R4
    • E2I9R5
    • F5H5U3
    • Q2M3H2
    • Q99861

    Protein attributes for HNF1A Gene

    631 amino acids
    Molecular mass:
    67356 Da
    Quaternary structure:
    • Binds DNA as a dimer. Interacts with PCBD1. Heterotetramer with PCBD1; formed by a dimer of dimers.

    Three dimensional structures from OCA and Proteopedia for HNF1A Gene

    Alternative splice isoforms for HNF1A Gene

neXtProt entry for HNF1A Gene

Post-translational modifications for HNF1A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HNF1A Gene

Domains & Families for HNF1A Gene

Gene Families for HNF1A Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HNF1 homeobox family.
  • Belongs to the HNF1 homeobox family.
genes like me logo Genes that share domains with HNF1A: view

Function for HNF1A Gene

Molecular function for HNF1A Gene

UniProtKB/Swiss-Prot Function:
Transcriptional activator that regulates the tissue specific expression of multiple genes, especially in pancreatic islet cells and in liver. Required for the expression of several liver specific genes. Binds to the inverted palindrome 5-GTTAATNATTAAC-3.

Phenotypes From GWAS Catalog for HNF1A Gene

Gene Ontology (GO) - Molecular Function for HNF1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA,ISS --
GO:0001221 transcription cofactor binding IEA --
genes like me logo Genes that share ontologies with HNF1A: view
genes like me logo Genes that share phenotypes with HNF1A: view

Human Phenotype Ontology for HNF1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HNF1A Gene

MGI Knock Outs for HNF1A:

Animal Model Products

CRISPR Products

miRNA for HNF1A Gene

miRTarBase miRNAs that target HNF1A

Transcription Factor Targets for HNF1A Gene

Selected GeneGlobe predicted Target genes for HNF1A
Targeted motifs for HNF1A Gene
HOMER Transcription Factor Regulatory Elements motif HNF1A
  • Consensus sequence: GGTTAAACATTAAC Submotif: canonical Cell Type: Liver GEO ID: GSE25694

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HNF1A

Clone Products

  • Addgene plasmids for HNF1A

No data available for Enzyme Numbers (IUBMB) for HNF1A Gene

Localization for HNF1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for HNF1A Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HNF1A gene
Compartment Confidence
nucleus 5
extracellular 2
mitochondrion 2
cytosol 2
plasma membrane 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HNF1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment IEA --
GO:0005634 nucleus IDA,IEA 15355349
GO:0005667 transcription factor complex IEA --
GO:0005737 cytoplasm IDA,IEA 15355349
GO:0032991 protein-containing complex IDA 11980910
genes like me logo Genes that share ontologies with HNF1A: view

Pathways & Interactions for HNF1A Gene

genes like me logo Genes that share pathways with HNF1A: view

SIGNOR curated interactions for HNF1A Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HNF1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001779 natural killer cell differentiation IDA 11301190
GO:0001824 blastocyst development IEA --
GO:0001889 liver development IEA --
GO:0001890 placenta development IEA --
GO:0006338 chromatin remodeling IEA --
genes like me logo Genes that share ontologies with HNF1A: view

Drugs & Compounds for HNF1A Gene

(25) Drugs for HNF1A Gene - From: DrugBank, ClinicalTrials, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
D-norleucine Experimental Pharma Target 0
Antibodies Pharma 7224
Autoantibodies Pharma 148
Immunoglobulins Pharma 7224

(17) Additional Compounds for HNF1A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HNF1A: view

Transcripts for HNF1A Gene

mRNA/cDNA for HNF1A Gene

(3) REFSEQ mRNAs :
(26) Additional mRNA sequences :
(17) Selected AceView cDNA sequences:
(16) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HNF1A Gene

HNF1 homeobox A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HNF1A

Clone Products

  • Addgene plasmids for HNF1A

Alternative Splicing Database (ASD) splice patterns (SP) for HNF1A Gene

No ASD Table

Relevant External Links for HNF1A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HNF1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HNF1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HNF1A Gene

This gene is overexpressed in Liver (x16.0), Kidney - Cortex (x11.2), Pancreas (x7.5), Colon - Transverse (x6.9), and Small Intestine - Terminal Ileum (x5.7).

Protein differential expression in normal tissues from HIPED for HNF1A Gene

This gene is overexpressed in Liver (60.4) and Prostate (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HNF1A Gene

Protein tissue co-expression partners for HNF1A Gene

NURSA nuclear receptor signaling pathways regulating expression of HNF1A Gene:


SOURCE GeneReport for Unigene cluster for HNF1A Gene:


mRNA Expression by UniProt/SwissProt for HNF1A Gene:

Tissue specificity: Liver.

Evidence on tissue expression from TISSUES for HNF1A Gene

  • Liver(4.8)
  • Intestine(2.9)
  • Kidney(2.9)
  • Pancreas(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HNF1A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • nervous
  • reproductive
  • urinary
Head and neck:
  • brain
  • ear
  • eye
  • head
  • heart
  • kidney
  • liver
  • pancreas
  • ovary
  • penis
  • placenta
  • uterus
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with HNF1A: view

Orthologs for HNF1A Gene

This gene was present in the common ancestor of chordates.

Orthologs for HNF1A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HNF1A 34 33
  • 100 (n)
(Canis familiaris)
Mammalia HNF1 34
  • 97 (a)
HNF1A 33
  • 92.08 (n)
(Bos Taurus)
Mammalia HNF1A 34 33
  • 92.23 (n)
(Rattus norvegicus)
Mammalia Hnf1a 33
  • 88.91 (n)
(Mus musculus)
Mammalia Hnf1a 16 34 33
  • 88.54 (n)
(Monodelphis domestica)
Mammalia HNF1A 34
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia HNF1A 34
  • 82 (a)
(Gallus gallus)
Aves HNF1A 34 33
  • 75.2 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia hnf1a 33
  • 68.38 (n)
African clawed frog
(Xenopus laevis)
Amphibia tcf1-A 33
(Danio rerio)
Actinopterygii hnf1a 34 33
  • 59.45 (n)
hnf1bb 34
  • 54 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
Species where no ortholog for HNF1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HNF1A Gene

Gene Tree for HNF1A (if available)
Gene Tree for HNF1A (if available)
Evolutionary constrained regions (ECRs) for HNF1A: view image

Paralogs for HNF1A Gene

Paralogs for HNF1A Gene

(4) SIMAP similar genes for HNF1A Gene using alignment to 20 proteins:

  • E2I9R4_HUMAN
  • E2I9R5_HUMAN
  • F5H0K0_HUMAN
  • F5H3Z5_HUMAN
  • F5H5U3_HUMAN
  • U3KQ02_HUMAN
genes like me logo Genes that share paralogs with HNF1A: view

Variants for HNF1A Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HNF1A Gene

The Ala-98/Val-98 polymorphism is associated with a reduction in glucose-induced serum C-peptide and insulin responses.

Sequence variations from dbSNP and Humsavar for HNF1A Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1030108448 uncertain-significance, Maturity-onset diabetes of the young 121,002,263(+) G/A/T 3_prime_UTR_variant
rs1057524898 uncertain-significance, Monogenic diabetes 120,993,609(+) T/A coding_sequence_variant, missense_variant
rs1057524908 pathogenic, Monogenic diabetes 120,993,687(+) C/CC coding_sequence_variant, frameshift
rs11065390 likely-benign, Maturity-onset diabetes of the young 121,001,795(+) G/A 3_prime_UTR_variant
rs115080759 not-provided, likely-benign, not specified, Monogenic diabetes 120,996,598(+) T/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for HNF1A Gene

Variant ID Type Subtype PubMed ID
esv2657723 CNV deletion 23128226
esv2746480 CNV deletion 23290073
esv2746481 CNV deletion 23290073
esv2746482 CNV deletion 23290073
esv2759917 CNV loss 17122850
esv3434592 CNV duplication 20981092
esv3580503 CNV loss 25503493
nsv1039216 CNV gain 25217958
nsv1124663 CNV duplication 24896259
nsv1141758 CNV insertion 24896259
nsv521928 CNV gain 19592680

Variation tolerance for HNF1A Gene

Residual Variation Intolerance Score: 53.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.29; 97.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HNF1A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

Disorders for HNF1A Gene

MalaCards: The human disease database

(23) MalaCards diseases for HNF1A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search HNF1A in MalaCards View complete list of genes associated with diseases


  • Hepatic adenomas familial (HEPAF) [MIM:142330]: Rare benign liver tumors of presumable epithelial origin that develop in an otherwise normal liver. Hepatic adenomas may be single or multiple. They consist of sheets of well-differentiated hepatocytes that contain fat and glycogen and can produce bile. Bile ducts or portal areas are absent. Kupffer cells, if present, are reduced in number and are non-functional. Conditions associated with adenomas are insulin-dependent diabetes mellitus and glycogen storage diseases (types 1 and 3). Note=The disease is caused by mutations affecting the gene represented in this entry. Bi-allelic inactivation of HNF1A, whether sporadic or associated with MODY3, may be an early step in the development of some hepatocellular carcinomas.
  • Maturity-onset diabetes of the young 3 (MODY3) [MIM:600496]: A form of diabetes that is characterized by an autosomal dominant mode of inheritance, onset in childhood or early adulthood (usually before 25 years of age), a primary defect in insulin secretion and frequent insulin-independence at the beginning of the disease. {ECO:0000269 PubMed:10078571, ECO:0000269 PubMed:10102714, ECO:0000269 PubMed:10482964, ECO:0000269 PubMed:10588527, ECO:0000269 PubMed:10966642, ECO:0000269 PubMed:12453420, ECO:0000269 PubMed:17573900, ECO:0000269 PubMed:8945470, ECO:0000269 PubMed:9032114, ECO:0000269 PubMed:9075818, ECO:0000269 PubMed:9075819, ECO:0000269 PubMed:9097962, ECO:0000269 PubMed:9166684, ECO:0000269 PubMed:9287053, ECO:0000269 PubMed:9392505, ECO:0000269 PubMed:9626139, ECO:0000269 PubMed:9754819}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Diabetes mellitus, insulin-dependent, 20 (IDDM20) [MIM:612520]: A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269 PubMed:10333057, ECO:0000269 PubMed:9313763, ECO:0000269 PubMed:9867222}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for HNF1A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HNF1A: view

No data available for Genatlas for HNF1A Gene

Publications for HNF1A Gene

  1. Common coding variants of the HNF1A gene are associated with multiple cardiovascular risk phenotypes in community-based samples of younger and older European-American adults: the Coronary Artery Risk Development in Young Adults Study and The Cardiovascular Health Study. (PMID: 20031592) Reiner AP … Nickerson DA (Circulation. Cardiovascular genetics 2009) 3 22 44 58
  2. Maturity-onset diabetes of the young in children with incidental hyperglycemia: a multicenter Italian study of 172 families. (PMID: 19564454) Lorini R … Italian Society of Pediatric Endocrinology and Diabetology (ISPED) Study Group (Diabetes care 2009) 3 22 44 58
  3. Identification of novel variants in the hepatocyte nuclear factor-1alpha gene in South Indian patients with maturity onset diabetes of young. (PMID: 19336507) Radha V … Mohan V (The Journal of clinical endocrinology and metabolism 2009) 3 22 44 58
  4. Prevalence of HNF1A (MODY3) mutations in a Norwegian population (the HUNT2 Study). (PMID: 18513305) Eide SA … Molven A (Diabetic medicine : a journal of the British Diabetic Association 2008) 3 22 44 58
  5. The type and the position of HNF1A mutation modulate age at diagnosis of diabetes in patients with maturity-onset diabetes of the young (MODY)-3. (PMID: 18003757) Bellanné-Chantelot C … Timsit J (Diabetes 2008) 3 22 44 58

Products for HNF1A Gene

  • Addgene plasmids for HNF1A

Sources for HNF1A Gene

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