Histidine triad proteins, such as HINT3, are nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides (Brenner, 2002 [PubMed 12119013]).[supplied by OMIM, Mar 2008] See more...

Aliases for HINT3 Gene

Aliases for HINT3 Gene

  • Histidine Triad Nucleotide Binding Protein 3 2 3 5
  • Histidine Triad Nucleotide-Binding Protein 3 3 4
  • HINT-3 3 4
  • HINT4 2 3
  • HIT-Like Protein 3
  • EC 3.-.-.- 4
  • FLJ33126 2
  • HINT3 5

External Ids for HINT3 Gene

Previous GeneCards Identifiers for HINT3 Gene

  • GC06P125937
  • GC06P126125
  • GC06P126258
  • GC06P126319
  • GC06P126277
  • GC06P123854

Summaries for HINT3 Gene

Entrez Gene Summary for HINT3 Gene

  • Histidine triad proteins, such as HINT3, are nucleotide hydrolases and transferases that act on the alpha-phosphate of ribonucleotides (Brenner, 2002 [PubMed 12119013]).[supplied by OMIM, Mar 2008]

GeneCards Summary for HINT3 Gene

HINT3 (Histidine Triad Nucleotide Binding Protein 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleotide binding and hydrolase activity. An important paralog of this gene is APTX.

UniProtKB/Swiss-Prot Summary for HINT3 Gene

Additional gene information for HINT3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HINT3 Gene

Genomics for HINT3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HINT3 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
GH06J125955 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.3 291 3.7 BRCA1 SP1 CREB1 GATAD2A CTCF ATF7 PRDM10 ZNF629 TFE3 LEF1 HINT3 TRMT11 CENPW NCOA7 RF00017-5766
GH06J125950 Promoter 0.6 EPDnew 600.4 -5.8 -5771 0.1 ZNF766 TRIM28 ZBTB33 TRIM24 HINT3 piR-36098-010 NCOA7
GH06J125788 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 13.8 -164.9 -164873 6.3 CTCF HNRNPL PRDM10 ZNF629 TFE3 IKZF1 ZNF692 RCOR2 POLR2A BACH1 NCOA7 lnc-HDDC2-11 HEY2 RNF217 HINT3 NCOA7-AS1 ENSG00000237742 TRMT11
GH06J125917 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13.2 -35.2 -35179 7.6 SP1 GATAD2A PRDM10 ZNF629 REST ZNF512 LEF1 SOX13 IKZF1 ZNF692 NCOA7 HINT3 HDDC2 NCOA7-AS1 HEY2 HSALNG0053307 piR-35729-057
GH06J125745 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.2 -207.6 -207569 9.2 RNF2 CTCF HNRNPL TEAD4 PRDM10 REST ZNF629 ZNF512 KDM1A ZNF692 HEY2 ENSG00000237742 LOC105377986 HDDC2 HINT3 NCOA7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HINT3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HINT3

Top Transcription factor binding sites by QIAGEN in the HINT3 gene promoter:
  • FOXO1
  • FOXO1a
  • GATA-1
  • GATA-2
  • GATA-3
  • Gfi-1
  • HSF2
  • IRF-7A
  • Nkx5-1
  • PPAR-alpha

Genomic Locations for HINT3 Gene

Genomic Locations for HINT3 Gene
23,475 bases
Plus strand
23,530 bases
Plus strand

Genomic View for HINT3 Gene

Genes around HINT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HINT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HINT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HINT3 Gene

Proteins for HINT3 Gene

  • Protein details for HINT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Histidine triad nucleotide-binding protein 3
    Protein Accession:
    Secondary Accessions:
    • B3KQ91
    • Q8N0Y9

    Protein attributes for HINT3 Gene

    182 amino acids
    Molecular mass:
    20361 Da
    Quaternary structure:
    • Forms dimers to octamers and even larger oligomer.

neXtProt entry for HINT3 Gene

Post-translational modifications for HINT3 Gene

  • Ubiquitination at Lys78, Lys115, and Lys179
  • Modification sites at PhosphoSitePlus

Other Protein References for HINT3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HINT3 Gene

Domains & Families for HINT3 Gene

Gene Families for HINT3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HINT3 Gene

  • Histidine triad (HIT) protein

Suggested Antigen Peptide Sequences for HINT3 Gene

GenScript: Design optimal peptide antigens:
  • Histidine triad nucleotide-binding protein 3 (HINT3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HINT family.
  • Belongs to the HINT family.
genes like me logo Genes that share domains with HINT3: view

Function for HINT3 Gene

Molecular function for HINT3 Gene

UniProtKB/Swiss-Prot Function:
Hydrolyzes phosphoramidate and acyl-adenylate substrates.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=1.5 uM for indolepropinoic acyl-adenylate {ECO:0000269|PubMed:17870088}; KM=22 uM for adenine {ECO:0000269|PubMed:17870088}; KM=29 uM for guanine {ECO:0000269|PubMed:17870088}; KM=32 uM for hypoxanthine {ECO:0000269|PubMed:17870088}; KM=121 uM for uracil {ECO:0000269|PubMed:17870088}; KM=181 uM for cytosine {ECO:0000269|PubMed:17870088}; Note=HINT3 prefers purine over pyrimidine-based substrates.;

Enzyme Numbers (IUBMB) for HINT3 Gene

Phenotypes From GWAS Catalog for HINT3 Gene

Gene Ontology (GO) - Molecular Function for HINT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003824 catalytic activity IEA --
GO:0016787 hydrolase activity IEA,IDA 17870088
GO:0042802 identical protein binding IDA 17870088
genes like me logo Genes that share ontologies with HINT3: view
genes like me logo Genes that share phenotypes with HINT3: view

Animal Model Products

CRISPR Products

miRNA for HINT3 Gene

miRTarBase miRNAs that target HINT3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HINT3

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HINT3 Gene

Localization for HINT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HINT3 Gene

Cytoplasm. Nucleus. Note=Localized as aggregates in the cytoplasm and the nucleus.

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 HINT3 gene
Compartment Confidence
nucleus 4
cytosol 3
extracellular 2
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HINT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IMP 17870088
GO:0005737 cytoplasm IMP 17870088
genes like me logo Genes that share ontologies with HINT3: view

Pathways & Interactions for HINT3 Gene

PathCards logo

SuperPathways for HINT3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HINT3 Gene


No data available for Pathways by source and SIGNOR curated interactions for HINT3 Gene

Drugs & Compounds for HINT3 Gene

No Compound Related Data Available

Transcripts for HINT3 Gene

mRNA/cDNA for HINT3 Gene

13 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HINT3

Alternative Splicing Database (ASD) splice patterns (SP) for HINT3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b
SP1: -
SP2: - -
SP3: -

Relevant External Links for HINT3 Gene

GeneLoc Exon Structure for

Expression for HINT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HINT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HINT3 Gene

This gene is overexpressed in Brain (10.5) and Frontal cortex (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HINT3 Gene

Protein tissue co-expression partners for HINT3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HINT3

SOURCE GeneReport for Unigene cluster for HINT3 Gene:


Evidence on tissue expression from TISSUES for HINT3 Gene

  • Eye(4.1)
  • Nervous system(2.7)
genes like me logo Genes that share expression patterns with HINT3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HINT3 Gene

Orthologs for HINT3 Gene

This gene was present in the common ancestor of animals.

Orthologs for HINT3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HINT3 30 31
  • 99.63 (n)
(Canis familiaris)
Mammalia HINT3 30 31
  • 89.86 (n)
(Bos Taurus)
Mammalia HINT3 30 31
  • 80.26 (n)
(Mus musculus)
Mammalia Hint3 30 17 31
  • 76.04 (n)
(Rattus norvegicus)
Mammalia Hint3 30
  • 74.71 (n)
(Ornithorhynchus anatinus)
Mammalia HINT3 31
  • 74 (a)
(Monodelphis domestica)
Mammalia -- 31
  • 57 (a)
-- 31
  • 54 (a)
(Gallus gallus)
Aves HINT3 30 31
  • 71.7 (n)
(Anolis carolinensis)
Reptilia HINT3 31
  • 63 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hint3 30
  • 65.78 (n)
(Danio rerio)
Actinopterygii hint3 30 31
  • 60.44 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG34015 30 31
  • 52.49 (n)
CG15362 31
  • 29 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007577 30
  • 49.75 (n)
(Caenorhabditis elegans)
Secernentea hint-3 31
  • 26 (a)
Species where no ortholog for HINT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)

Evolution for HINT3 Gene

Gene Tree for HINT3 (if available)
Gene Tree for HINT3 (if available)
Evolutionary constrained regions (ECRs) for HINT3: view image

Paralogs for HINT3 Gene

Paralogs for HINT3 Gene

genes like me logo Genes that share paralogs with HINT3: view

Variants for HINT3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HINT3 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs2295005 - p.Gly36Ala

Additional dbSNP identifiers (rs#s) for HINT3 Gene

Structural Variations from Database of Genomic Variants (DGV) for HINT3 Gene

Variant ID Type Subtype PubMed ID
esv2732681 CNV deletion 23290073
nsv1019490 CNV loss 25217958
nsv1022677 CNV gain 25217958
nsv1025069 CNV loss 25217958
nsv830796 CNV loss 17160897

Variation tolerance for HINT3 Gene

Residual Variation Intolerance Score: 59.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.75; 15.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HINT3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HINT3 Gene

Disorders for HINT3 Gene

No disorders were found for HINT3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HINT3 Gene

Publications for HINT3 Gene

  1. Evidence that human histidine triad nucleotide binding protein 3 (Hint3) is a distinct branch of the histidine triad (HIT) superfamily. (PMID: 17870088) Chou TF … Wagner CR (Journal of molecular biology 2007) 3 4 23
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases. (PMID: 12119013) Brenner C (Biochemistry 2002) 3 4
  4. Adenosine monophosphoramidase activity of Hint and Hnt1 supports function of Kin28, Ccl1, and Tfb3. (PMID: 11805111) Bieganowski P … Brenner C (The Journal of biological chemistry 2002) 2 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for HINT3 Gene

Sources for HINT3 Gene