Gene Gene information from NCBI Gene database.
Entrez ID 6927
Gene name HNF1 homeobox A
Gene symbol HNF1A
Synonyms (NCBI Gene)
HNF-1-alphaHNF-1AHNF1HNF1alphaHNF4AIDDM20LFB1MODY3TCF-1TCF1
Chromosome 12
Chromosome location 12q24.31
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
SNPs SNP information provided by dbSNP.
95
SNP ID Visualize variation Clinical significance Consequence
rs1169288 A>C,T Benign, risk-factor Coding sequence variant, missense variant
rs1169305 A>C,G,T Benign, not-provided, pathogenic Coding sequence variant, missense variant
rs137853236 C>T Pathogenic Coding sequence variant, missense variant
rs137853237 A>G Pathogenic Coding sequence variant, missense variant
rs137853238 G>A Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
44
miRTarBase ID miRNA Experiments Reference
MIRT004646 hsa-miR-194-5p Review 20029422
MIRT044838 hsa-miR-320a CLASH 23622248
MIRT437966 hsa-miR-15b-5p qRT-PCRLuciferase reporter assayWestern blot 24705650
MIRT437966 hsa-miR-15b-5p qRT-PCRLuciferase reporter assayWestern blot 24705650
MIRT437966 hsa-miR-15b-5p qRT-PCRLuciferase reporter assayWestern blot 24705650
Transcription factors Transcription factors information provided by TRRUST V2 database.
3
Transcription factor Regulation Reference
HNF4A Unknown 9792724
RXRA Unknown 11027556
ZHX2 Unknown 18194454
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
35
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin ISA
GO:0000976 Function Transcription cis-regulatory region binding IDA 12453420, 15961790
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
142410 11621 ENSG00000135100
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P20823
Protein name Hepatocyte nuclear factor 1-alpha (HNF-1-alpha) (HNF-1A) (Liver-specific transcription factor LF-B1) (LFB1) (Transcription factor 1) (TCF-1)
Protein function Transcriptional activator that regulates the tissue specific expression of multiple genes, especially in pancreatic islet cells and in liver (By similarity). Binds to the inverted palindrome 5'-GTTAATNATTAAC-3' (PubMed:10966642, PubMed:12453420)
PDB 1IC8 , 2GYP , 8PI7 , 8PI8 , 8PI9 , 8PIA
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF04814 HNF-1_N 8 168 Hepatocyte nuclear factor 1 (HNF-1), N terminus Family
PF04812 HNF-1B_C 282 540 Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus Family
PF04813 HNF-1A_C 542 630 Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus Family
Tissue specificity TISSUE SPECIFICITY: Liver.
Sequence
Sequence length 631
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  Maturity onset diabetes of the young  
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
72
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Clear cell carcinoma of kidney Pathogenic rs587776825 RCV000016063
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Diabetes mellitus Pathogenic; Likely pathogenic rs893256143, rs765432081, rs779184183, rs1877113317, rs1877168655, rs1876671395, rs768753432, rs199890776 RCV001175316
RCV001175312
RCV001175315
RCV001172532
RCV001172533
View all (3 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Diabetes mellitus type 1 Pathogenic rs587780357, rs587776825 RCV000117232
RCV000117225
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
DiGeorge syndrome Pathogenic rs587776825 RCV003445070
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Breast carcinoma Benign ClinVar
GWAS catalog
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
CARCINOMA, RENAL CELL CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARDIOVASCULAR DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 20930648
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma LHGDN 12701690, 17393984
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 21348892, 27757985
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Of Esophagus Esophageal Cancer BEFREE 25863539
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 28952142, 29469192, 30848476
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of pancreas Pancreatic adenocarcinoma BEFREE 30867652
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma, Endometrioid Endometrial Cancer BEFREE 19843521
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma LHGDN 12355088, 17049664
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 23485860, 25195525, 25569436, 26274031, 26676820, 27015136, 30121369
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 11389074, 12086873, 14660579, 15574752, 16885356, 17952864, 18774639, 23129580, 30110600
★☆☆☆☆
Found in Text Mining only