Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HAL Gene

Aliases for HAL Gene

  • Histidine Ammonia-Lyase 2 3 5
  • EC 4 63
  • Histidase 3 4
  • HIS 3 4
  • EC 4.3.1 63
  • HSTD 3

External Ids for HAL Gene

Previous HGNC Symbols for HAL Gene

  • HIS

Previous GeneCards Identifiers for HAL Gene

  • GC12M095787
  • GC12M096730
  • GC12M096300
  • GC12M094869
  • GC12M093429
  • GC12M096366

Summaries for HAL Gene

Entrez Gene Summary for HAL Gene

  • Histidine ammonia-lyase is a cytosolic enzyme catalyzing the first reaction in histidine catabolism, the nonoxidative deamination of L-histidine to trans-urocanic acid. Histidine ammonia-lyase defects cause histidinemia which is characterized by increased histidine and histamine and decreased urocanic acid in body fluids. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

GeneCards Summary for HAL Gene

HAL (Histidine Ammonia-Lyase) is a Protein Coding gene. Diseases associated with HAL include Histidinemia and Histidine Metabolism Disease. Among its related pathways are Histidine metabolism and Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism. GO annotations related to this gene include histidine ammonia-lyase activity and ammonia-lyase activity.

Gene Wiki entry for HAL Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HAL Gene

Genomics for HAL Gene

Regulatory Elements for HAL Gene

Enhancers for HAL Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around HAL on UCSC Golden Path with GeneCards custom track

Promoters for HAL Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HAL on UCSC Golden Path with GeneCards custom track

Genomic Location for HAL Gene

95,972,662 bp from pter
95,996,365 bp from pter
23,704 bases
Minus strand

Genomic View for HAL Gene

Genes around HAL on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for HAL Gene

Proteins for HAL Gene

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

    Protein Symbol:
    Recommended name:
    Histidine ammonia-lyase
    Protein Accession:
    Secondary Accessions:
    • B4DQC1
    • B4E0V8
    • F5GXF2
    • F5H1U5
    • Q4VB92
    • Q4VB93

    Protein attributes for HAL Gene

    657 amino acids
    Molecular mass:
    72698 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for HAL Gene


neXtProt entry for HAL Gene

Proteomics data for HAL Gene at MOPED

Post-translational modifications for HAL Gene

  • Contains an active site 4-methylidene-imidazol-5-one (MIO), which is formed autocatalytically by cyclization and dehydration of residues Ala-Ser-Gly.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for HAL Gene

Protein Domains for HAL Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PAL/histidase family.
  • Belongs to the PAL/histidase family.
genes like me logo Genes that share domains with HAL: view

No data available for Gene Families for HAL Gene

Function for HAL Gene

Molecular function for HAL Gene

GENATLAS Biochemistry:
histidine ammonia lyase (histidase),histidine catabolism
UniProtKB/Swiss-Prot CatalyticActivity:
L-histidine = urocanate + NH(3).

Enzyme Numbers (IUBMB) for HAL Gene

Gene Ontology (GO) - Molecular Function for HAL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004397 histidine ammonia-lyase activity EXP,IEA 15806399
genes like me logo Genes that share ontologies with HAL: view
genes like me logo Genes that share phenotypes with HAL: view

Human Phenotype Ontology for HAL Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for HAL Gene

Localization for HAL Gene

Subcellular locations from

Jensen Localization Image for HAL Gene COMPARTMENTS Subcellular localization image for HAL gene
Compartment Confidence
cytosol 5
mitochondrion 2
nucleus 2
cytoskeleton 1
extracellular 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for HAL Gene

Pathways & Interactions for HAL Gene

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

UniProtKB/Swiss-Prot P42357-HUTH_HUMAN

  • Pathway: Amino-acid degradation; L-histidine degradation into L-glutamate; N-formimidoyl-L-glutamate from L-histidine: step 1/3.

Interacting Proteins for HAL Gene

Gene Ontology (GO) - Biological Process for HAL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006548 histidine catabolic process IEA,TAS --
GO:0008152 metabolic process IEA --
GO:0019556 histidine catabolic process to glutamate and formamide IEA --
GO:0034641 cellular nitrogen compound metabolic process TAS --
genes like me logo Genes that share ontologies with HAL: view

No data available for SIGNOR curated interactions for HAL Gene

Drugs & Compounds for HAL Gene

(11) Drugs for HAL Gene - From: DrugBank, ClinicalTrials, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Histidine Approved Nutra Target 0
urocanic acid Experimental Pharma 0
Methyl 5-aminolevulinate Pharma 53
Photosensitizing Agents Pharma 448

(4) Additional Compounds for HAL Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Ammonia anhydrous
  • Ammonia inhalant
  • Ammonia solution strong [usan]
  • Ammonia water
  • Ammoniak
genes like me logo Genes that share compounds with HAL: view

Transcripts for HAL Gene

Unigene Clusters for HAL Gene

Histidine ammonia-lyase:
Representative Sequences:

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

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18a · 18b ^ 19 ^ 20 ^ 21a · 21b ^
SP1: - -
SP2: - - - -
SP3: -

ExUns: 22a · 22b

Relevant External Links for HAL Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HAL Gene

mRNA expression in normal human tissues for HAL Gene

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

This gene is overexpressed in Liver (x27.8), Whole Blood (x12.2), and Skin - Sun Exposed (Lower leg) (x5.0).

Protein differential expression in normal tissues from HIPED for HAL Gene

This gene is overexpressed in Fetal Liver (29.3), Saliva (20.6), and Liver (12.5).

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

SOURCE GeneReport for Unigene cluster for HAL Gene Hs.190783

genes like me logo Genes that share expression patterns with HAL: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for HAL Gene

Orthologs for HAL Gene

This gene was present in the common ancestor of animals.

Orthologs for HAL Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia HAL 35
  • 90.01 (n)
  • 95.13 (a)
HAL 36
  • 95 (a)
(Canis familiaris)
Mammalia HAL 35
  • 90.01 (n)
  • 94.98 (a)
HAL 36
  • 95 (a)
(Mus musculus)
Mammalia Hal 35
  • 87.42 (n)
  • 93.76 (a)
Hal 16
Hal 36
  • 94 (a)
(Pan troglodytes)
Mammalia HAL 35
  • 99.39 (n)
  • 99.24 (a)
HAL 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Hal 35
  • 87.67 (n)
  • 93.91 (a)
(Monodelphis domestica)
Mammalia HAL 36
  • 91 (a)
(Ornithorhynchus anatinus)
Mammalia HAL 36
  • 90 (a)
(Gallus gallus)
Aves HAL 35
  • 78.29 (n)
  • 89.04 (a)
HAL 36
  • 81 (a)
(Anolis carolinensis)
Reptilia HAL 36
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hal.1 35
  • 72.98 (n)
  • 80.46 (a)
Str.16849 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.2256 35
(Danio rerio)
Actinopterygii hal 35
  • 71.97 (n)
  • 82.06 (a)
hal 36
  • 80 (a)
(Caenorhabditis elegans)
Secernentea F47B10.2 37
  • 54 (a)
haly-1 35
  • 56.03 (n)
  • 57 (a)
haly-1 36
  • 53 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11334 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 60 (a)
Species with no ortholog for HAL:
  • 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)
  • 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)

Evolution for HAL Gene

Gene Tree for HAL (if available)
Gene Tree for HAL (if available)

Paralogs for HAL Gene

No data available for Paralogs for HAL Gene

Variants for HAL Gene

Sequence variations from dbSNP and Humsavar for HAL Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs7297245 - 95,980,836(+) AGAAA(C/T)TGTCT reference, missense
VAR_022915 Histidinemia (HISTID)
VAR_022916 Histidinemia (HISTID)
VAR_022917 Histidinemia (HISTID)
VAR_022918 Histidinemia (HISTID)

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

Variant ID Type Subtype PubMed ID
nsv7234 OTHER Inversion 18451855
nsv523292 CNV Gain 19592680

Variation tolerance for HAL Gene

Residual Variation Intolerance Score: 82% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.66; 45.83% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HAL Gene

Human Gene Mutation Database (HGMD)

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

Disorders for HAL Gene

MalaCards: The human disease database

(2) MalaCards diseases for HAL Gene - From: GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
  • histidinuria
histidine metabolism disease
  • disturbances of histidine metabolism
- elite association - COSMIC cancer census association via MalaCards
Search HAL in MalaCards View complete list of genes associated with diseases


  • Histidinemia (HISTID) [MIM:235800]: Autosomal recessive disease characterized by increased histidine and histamine as well as decreased urocanic acid in body fluids. {ECO:0000269 PubMed:15806399}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for HAL Gene


Relevant External Links for HAL

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with HAL: view

Publications for HAL Gene

  1. Molecular cloning and structural characterization of the human histidase gene (HAL). (PMID: 8530107) Suchi M. … Wada Y. (Genomics 1995) 3 4 23 67
  2. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. (PMID: 17185227) Watts K.T. … Schmidt-Dannert C. (Chem. Biol. 2006) 23 25 26
  3. Inhibition of histidine ammonia lyase by heteroaryl-alanines and acrylates. (PMID: 17193285) Katona A. … RActey J. (Chem. Biodivers. 2006) 23 25 26
  4. Kinetic analysis of the reactions catalyzed by histidine and phenylalanine ammonia lyases. (PMID: 17191848) Viergutz S. … RActey J. (Chem. Biodivers. 2004) 23 25 26
  5. Histidase expression in human epidermal keratinocytes: regulation by differentiation status and all-trans retinoic acid. (PMID: 18280705) Eckhart L. … Tschachler E. (J. Dermatol. Sci. 2008) 3 23

Products for HAL Gene

Sources for HAL Gene