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HAL histidine ammonia-lyase [ Homo sapiens (human) ]

Gene ID: 3034, updated on 3-Nov-2024

Summary

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Official Symbol
HALprovided by HGNC
Official Full Name
histidine ammonia-lyaseprovided by HGNC
Primary source
HGNC:HGNC:4806
See related
Ensembl:ENSG00000084110 MIM:609457; AllianceGenome:HGNC:4806
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HIS; HSTD
Summary
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]
Expression
Biased expression in skin (RPKM 20.5), liver (RPKM 18.5) and 2 other tissues See more
Orthologs
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Genomic context

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See HAL in Genome Data Viewer
Location:
12q23.1
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (95972662..95996344, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (95946669..95970341, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (96366440..96390122, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 38 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96301545-96302055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96302056-96302565 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:96322471-96322972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96350128-96350641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96350642-96351154 Neighboring gene amidohydrolase domain containing 1 Neighboring gene AMDHD1 eExon liver enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96363883-96364528 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:96364529-96365174 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31139 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 12:96379806 Neighboring gene uncharacterized LOC102723340 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31163 Neighboring gene Sharpr-MPRA regulatory region 10760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6820 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31173 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31174 Neighboring gene leukotriene A4 hydrolase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31179 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6822 Neighboring gene tRNA-Asp (anticodon GTC) 2-8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Molecular cloning and structural characterization of the human histidase gene (HAL). Suchi M, et al. Genomics, 1995 Sep 1. PMID 8530107
  2. The role of single nucleotide variant rs3819817 of the Histidine Ammonia-Lyase gene and 25-Hydroxyvitamin D on bone mineral density, adiposity markers, and skin pigmentation, in Mexican population. Rivera-Paredez B, et al. J Endocrinol Invest, 2023 Sep. PMID 36862244
  3. Association of Rare Loss-Of-Function Alleles in HAL, Serum Histidine: Levels and Incident Coronary Heart Disease. Yu B, et al. Circ Cardiovasc Genet, 2015 Apr. PMID 25575548, Free PMC Article
  4. A role for ultraviolet radiation immunosuppression in non-melanoma skin cancer as evidenced by gene-environment interactions. Welsh MM, et al. Carcinogenesis, 2008 Oct. PMID 18641401, Free PMC Article
  5. Molecular cloning of a cDNA encoding human histidase. Suchi M, et al. Biochim Biophys Acta, 1993 Nov 16. PMID 7916645

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The role of single nucleotide variant rs3819817 of the Histidine Ammonia-Lyase gene and 25-Hydroxyvitamin D on bone mineral density, adiposity markers, and skin pigmentation, in Mexican population.
    Title: The role of single nucleotide variant rs3819817 of the Histidine Ammonia-Lyase gene and 25-Hydroxyvitamin D on bone mineral density, adiposity markers, and skin pigmentation, in Mexican population.
  2. In the analysis of the genotype tissue expression (GTEx) project datasets, HAL rs17676826 C and NOXRED1 rs8012548 G alleles were significantly associated with their mRNA expression levels in sun-exposed skin of the lower leg (P = 6.62 x 10(-6) and 1.37 x 10(-7) , respectively) and in sun-not-exposed suprapubic skin (P < .001 and 1.43 x 10(-8) , respectively).
    Title: Genetic variants in glutamine metabolic pathway genes predict cutaneous melanoma-specific survival.
  3. Three LoF mutations in HAL were associated with increased histidine levels, which in turn were shown to be inversely related to the risk of CHD among both African Americans and European Americans.
    Title: Association of Rare Loss-Of-Function Alleles in HAL, Serum Histidine: Levels and Incident Coronary Heart Disease.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: New genetic associations detected in a host response study to hepatitis B vaccine.
  5. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: A role for ultraviolet radiation immunosuppression in non-melanoma skin cancer as evidenced by gene-environment interactions.
  6. histidase is upregulated during keratinocyte differentiation and that all-trans retinoic acid but not UV irradiation modulates the expression level
    Title: Histidase expression in human epidermal keratinocytes: regulation by differentiation status and all-trans retinoic acid.
  7. This evidence supports that the Hal gene is turned on by glucocorticoids and by glucagon either via PKC or PKA, but prefers the PKA pathway.
    Title: Regulation by glucagon of the rat histidase gene promoter in cultured rat hepatocytes and human hepatoblastoma cells.
  8. This report describes the first mutations occurring in the coding region of the histidase structural gene in patients with histidinemia.
    Title: Molecular characterization of histidinemia: identification of four missense mutations in the histidase gene.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Histidinemia
MedGen: C0220992 OMIM: 235800 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histidine ammonia-lyase activity EXP
Inferred from Experiment
more info
 PubMed 
enables histidine ammonia-lyase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in L-histidine catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in L-histidine catabolic process TAS
Traceable Author Statement
more info
  
involved_in L-histidine catabolic process to glutamate and formamide IEA
Inferred from Electronic Annotation
more info
  
involved_in L-histidine catabolic process to glutamate and formate IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
histidine ammonia-lyase
Names
histidase
NP_001245262.1
NP_001245263.1
NP_002099.1
XP_011536551.1
XP_016874735.1
XP_054227876.1
XP_054227877.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008180.1 RefSeqGene

    Range
    4950..28632
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001258333.2 → NP_001245262.1  histidine ammonia-lyase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC126174, AI248003, AK303544, AL596896, D16626
    Consensus CDS
    CCDS58264.1
    UniProtKB/Swiss-Prot
    P42357
    Related
    ENSP00000446364.1, ENST00000541929.5
    Conserved Domains (1) summary
    TIGR01225
    Location:1 → 417
    hutH; histidine ammonia-lyase

  2. NM_001258334.2 → NP_001245263.1  histidine ammonia-lyase isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC126174, AI248003, AK298736
    Consensus CDS
    CCDS58265.1
    UniProtKB/Swiss-Prot
    P42357
    Related
    ENSP00000440861.1, ENST00000538703.5
    Conserved Domains (2) summary
    TIGR01225
    Location:114 → 588
    hutH; histidine ammonia-lyase
    pfam12053
    Location:15 → 88
    DUF3534; Domain of unknown function (DUF3534)

  3. NM_002108.4 → NP_002099.1  histidine ammonia-lyase isoform 1

    See identical proteins and their annotated locations for NP_002099.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC126174, AI248003, AL596896, D16626
    Consensus CDS
    CCDS9058.1
    UniProtKB/Swiss-Prot
    B4DQC1, B4E0V8, F5GXF2, F5H1U5, P42357, Q4VB92, Q4VB93
    Related
    ENSP00000261208.3, ENST00000261208.8
    Conserved Domains (2) summary
    TIGR01225
    Location:114 → 625
    hutH; histidine ammonia-lyase
    pfam12053
    Location:15 → 88
    DUF3534; Domain of unknown function (DUF3534)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    95972662..95996344 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538249.3 → XP_011536551.1  histidine ammonia-lyase isoform X1

    Conserved Domains (1) summary
    cl00013
    Location:2 → 341
    Lyase_I_like; Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions

  2. XM_017019246.1 → XP_016874735.1  histidine ammonia-lyase isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    95946669..95970341 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371901.1 → XP_054227876.1  histidine ammonia-lyase isoform X1

  2. XM_054371902.1 → XP_054227877.1  histidine ammonia-lyase isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P42357.1 GenPept UniProtKB/Swiss-Prot:P42357

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