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Aliases for HAL Gene

Aliases for HAL Gene

  • Histidine Ammonia-Lyase 2 3 3 5
  • Histidase 3 4
  • HIS 3 4
  • EC 4
  • 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 degradation and Metabolism. Gene Ontology (GO) annotations related to this gene include histidine ammonia-lyase activity and ammonia-lyase activity.

Gene Wiki entry for HAL Gene

Additional gene information for HAL Gene

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

Genomics for HAL Gene

GeneHancer (GH) Regulatory Elements for HAL Gene

Promoters and enhancers for HAL 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
GH12J095994 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 673.1 +0.4 364 2.4 FOXA2 MLX ARID4B DMAP1 ETS1 YY1 SLC30A9 ELK1 ATF7 NFKBIZ HAL LOC102723340 AMDHD1 CCDC38 GC12M095983
GH12J096003 Promoter 0.5 EPDnew 650.4 -6.7 -6684 0.1 HAL LOC102723340 ENSG00000257715 LTA4H
GH12J096033 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 30.5 -38.9 -38873 2.9 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 TRD-GTC2-8 LTA4H HAL LOC102723340 NR2C1 ENSG00000258272 ENSG00000258313 ENSG00000202368 ENSG00000257470 NEDD1
GH12J095972 Enhancer 0.9 ENCODE 34 +22.9 22877 2.8 FOXA2 MLX ARID4B YY1 SLC30A9 RXRA SP5 MXD4 PPARG KAT8 HAL AMDHD1 CCDC38 LOC102723340 GC12M095961 GC12M095983
GH12J096036 Enhancer 0.9 ENCODE dbSUPER 32.8 -41.1 -41066 1.4 HDAC1 PKNOX1 TEAD4 TAL1 CEBPG IRF9 TCF12 POLR2A CBFA2T2 TRIM24 TRD-GTC2-8 HAL LOC102723340 LTA4H
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HAL on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HAL gene promoter:
  • Nkx2-5
  • Sp1
  • deltaCREB
  • CREB
  • GR-alpha
  • GR
  • POU3F2

Genomic Locations for HAL Gene

Genomic Locations for HAL Gene
23,704 bases
Minus strand
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

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

No data available for DME Specific Peptides for HAL Gene

Domains & Families for HAL Gene

Gene Families for HAL Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

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

Function for HAL Gene

Molecular function for HAL Gene

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

Enzyme Numbers (IUBMB) for HAL Gene

Phenotypes From GWAS Catalog 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 15806399
GO:0016829 lyase activity IEA --
GO:0016841 ammonia-lyase activity IEA --
genes like me logo Genes that share ontologies with HAL: view
genes like me logo Genes that share phenotypes with HAL: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

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

Localization for HAL 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 HAL gene
Compartment Confidence
cytosol 5
mitochondrion 2
nucleus 2
extracellular 1
cytoskeleton 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HAL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with HAL: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot 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.

Gene Ontology (GO) - Biological Process for HAL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006547 histidine metabolic process IEA --
GO:0006548 histidine catabolic process TAS --
GO:0019556 histidine catabolic process to glutamate and formamide IEA --
GO:0019557 histidine catabolic process to glutamate and formate IEA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Histidine Approved Nutra Target 50
Aminolevulinic acid Approved Pharma 170
Ammonia Approved Pharma 0
Dermatologic Agents Pharma 6201
Methyl 5-aminolevulinate Pharma 62

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
urocanic acid
  • (2E)-3-(1H-Imidazol-4-yl)acrylic acid
  • (e)-3-(1H-Imidazol-4-yl)-2-propenoic acid
  • (2E)-3-(1H-Imidazol-4-yl)acrylate
  • Urocanate
  • (e)-3-(1H-Imidazol-4-yl)-2-propenoate
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:

CRISPR Products

Inhibitory RNA Products

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

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for HAL Gene

NURSA nuclear receptor signaling pathways regulating expression of HAL Gene:


SOURCE GeneReport for Unigene cluster for HAL Gene:


Evidence on tissue expression from TISSUES for HAL Gene

  • Liver(4.6)
  • Skin(2.8)
  • Intestine(2.3)
  • Stomach(2.3)
genes like me logo Genes that share expression patterns with HAL: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia HAL 34 33
  • 99.39 (n)
(Monodelphis domestica)
Mammalia HAL 34
  • 91 (a)
(Canis familiaris)
Mammalia HAL 34 33
  • 90.01 (n)
(Bos Taurus)
Mammalia HAL 34 33
  • 90.01 (n)
(Ornithorhynchus anatinus)
Mammalia HAL 34
  • 90 (a)
(Rattus norvegicus)
Mammalia Hal 33
  • 87.67 (n)
(Mus musculus)
Mammalia Hal 16 34 33
  • 87.42 (n)
(Gallus gallus)
Aves HAL 34 33
  • 78.29 (n)
(Anolis carolinensis)
Reptilia HAL 34
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hal.1 33
  • 72.98 (n)
Str.16849 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.2256 33
(Danio rerio)
Actinopterygii hal 34 33
  • 71.97 (n)
(Caenorhabditis elegans)
Secernentea haly-1 34 33
  • 56.03 (n)
F47B10.2 35
  • 54 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 60 (a)
Cin.11334 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11334 33
Species where no ortholog for HAL 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)
  • 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)
Evolutionary constrained regions (ECRs) for HAL: view image

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 Variation AA Info Type
rs1002314133 uncertain-significance, Histidinemia 95,972,684(-) C/T 3_prime_UTR_variant
rs1059844 benign, Histidinemia 95,972,991(-) T/G 3_prime_UTR_variant
rs1059845 likely-benign, Histidinemia 95,972,920(-) G/A/C 3_prime_UTR_variant
rs11108364 likely-benign, Histidinemia 95,987,197(-) A/G/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant, synonymous_variant
rs11108369 likely-benign, Histidinemia 95,996,123(-) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
esv3630445 CNV gain 21293372
nsv523292 CNV gain 19592680
nsv7234 OTHER inversion 18451855

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)

Additional Variant Information for HAL Gene

Human Gene Mutation Database (HGMD)
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 HAL Gene

Disorders for HAL Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
  • histidine ammonia-lyase deficiency
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


Additional Disease Information for HAL

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 HAL: view

Publications for HAL Gene

  1. A role for ultraviolet radiation immunosuppression in non-melanoma skin cancer as evidenced by gene-environment interactions. (PMID: 18641401) Welsh MM … Nelson HH (Carcinogenesis 2008) 3 22 44 58
  2. Molecular characterization of histidinemia: identification of four missense mutations in the histidase gene. (PMID: 15806399) Kawai Y … Suchi M (Human genetics 2005) 3 4 22 58
  3. Molecular cloning and structural characterization of the human histidase gene (HAL). (PMID: 8530107) Suchi M … Wada Y (Genomics 1995) 3 4 22 58
  4. Molecular cloning of a cDNA encoding human histidase. (PMID: 7916645) Suchi M … Takagi Y (Biochimica et biophysica acta 1993) 3 4 22 58
  5. Histidase expression in human epidermal keratinocytes: regulation by differentiation status and all-trans retinoic acid. (PMID: 18280705) Eckhart L … Tschachler E (Journal of dermatological science 2008) 3 22 58

Products for HAL Gene

Sources for HAL Gene

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