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    HACL1 2-hydroxyacyl-CoA lyase 1 [ Homo sapiens (human) ]

    Gene ID: 26061, updated on 10-Dec-2024

    Summary

    Official Symbol
    HACL1provided by HGNC
    Official Full Name
    2-hydroxyacyl-CoA lyase 1provided by HGNC
    Primary source
    HGNC:HGNC:17856
    See related
    Ensembl:ENSG00000131373 MIM:604300; AllianceGenome:HGNC:17856
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HPCL; HPCL2; PHYH2; 2-HPCL
    Summary
    Enables several functions, including 2-hydroxyacyl-CoA lyase activity; ATP binding activity; and cation binding activity. Involved in fatty acid alpha-oxidation; phytanic acid metabolic process; and protein targeting to peroxisome. Located in nucleoplasm and peroxisome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in duodenum (RPKM 25.3), testis (RPKM 14.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HACL1 in Genome Data Viewer
    Location:
    3p25.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (15560699..15601569, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (15563097..15603888, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (15602206..15643076, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene collagen like tail subunit of asymmetric acetylcholinesterase Neighboring gene microRNA 4270 Neighboring gene RNA, 7SL, cytoplasmic 110, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:15642981-15643623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:15688189-15688722 Neighboring gene Sharpr-MPRA regulatory region 6531 Neighboring gene biotinidase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_65637 Neighboring gene ankyrin repeat domain 28 Neighboring gene microRNA 3134 Neighboring gene RNA, 7SL, cytoplasmic 4, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: COLQ

    Clone Names

    • FLJ55041

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 2-hydroxyacyl-CoA lyase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables 2-hydroxyphytanoyl-CoA lyase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables carbon-carbon lyase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables carbon-carbon lyase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables thiamine pyrophosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables thiamine pyrophosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables thiamine pyrophosphate binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in peroxisomal matrix TAS
    Traceable Author Statement
    more info
     
    is_active_in peroxisome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in peroxisome IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    2-hydroxyacyl-CoA lyase 1
    Names
    1600020H07Rik
    2-hydroxyphytanol-CoA lyase
    2-hydroxyphytanoyl-CoA lyase
    phytanoyl-CoA 2-hydroxylase 2
    phytanoyl-CoA hydroxylase 2
    NP_001271342.1
    NP_001271344.1
    NP_001271345.1
    NP_036392.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001284413.2NP_001271342.1  2-hydroxyacyl-CoA lyase 1 isoform b

      See identical proteins and their annotated locations for NP_001271342.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AA643224, AC027129, AK301546, DA609383
      Consensus CDS
      CCDS68360.1
      UniProtKB/TrEMBL
      B4DXR1
      Related
      ENSP00000390699.2, ENST00000456194.6
      Conserved Domains (1) summary
      PRK09259
      Location:7536
      PRK09259; putative oxalyl-CoA decarboxylase; Validated
    2. NM_001284415.2NP_001271344.1  2-hydroxyacyl-CoA lyase 1 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons in the central coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.
      Source sequence(s)
      AA643224, AC027129, AJ131753, AK302086, BC001627, DA609383
      Consensus CDS
      CCDS68362.1
      UniProtKB/TrEMBL
      B4DXR1
      Related
      ENSP00000404883.2, ENST00000457447.6
      Conserved Domains (4) summary
      cd07035
      Location:19146
      TPP_PYR_POX_like; Pyrimidine (PYR) binding domain of POX and related proteins
      PRK09259
      Location:7503
      PRK09259; putative oxalyl-CoA decarboxylase; Validated
      cd02004
      Location:317500
      TPP_BZL_OCoD_HPCL; Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL ...
      pfam00205
      Location:180305
      TPP_enzyme_M; Thiamine pyrophosphate enzyme, central domain
    3. NM_001284416.2NP_001271345.1  2-hydroxyacyl-CoA lyase 1 isoform d

      See identical proteins and their annotated locations for NP_001271345.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three alternate exons that result in the loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AA643224, AC027129, AK301990, DA609383
      Consensus CDS
      CCDS68361.1
      UniProtKB/TrEMBL
      B4DXR1
      Related
      ENSP00000403656.2, ENST00000451445.6
      Conserved Domains (4) summary
      cd07035
      Location:19103
      TPP_PYR_POX_like; Pyrimidine (PYR) binding domain of POX and related proteins
      PRK09259
      Location:7481
      PRK09259; putative oxalyl-CoA decarboxylase; Validated
      cd02004
      Location:295478
      TPP_BZL_OCoD_HPCL; Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL ...
      pfam00205
      Location:124250
      TPP_enzyme_M; Thiamine pyrophosphate enzyme, central domain
    4. NM_012260.4NP_036392.2  2-hydroxyacyl-CoA lyase 1 isoform a

      See identical proteins and their annotated locations for NP_036392.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AA643224, AC027129, AJ131753, BC001627, DA609383
      Consensus CDS
      CCDS2627.1
      UniProtKB/Swiss-Prot
      B4DWI1, B4DXI5, E9PEN4, Q9BV42, Q9P0A2, Q9UJ83
      UniProtKB/TrEMBL
      B4DXR1
      Related
      ENSP00000323811.5, ENST00000321169.10
      Conserved Domains (1) summary
      cl28198
      Location:7563
      IlvB; Acetolactate synthase large subunit or other thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism]

    RNA

    1. NR_104315.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks two alternate exons in the central region, compared to variant 1. This variant is represented as non-coding because use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA643224, AC027129, BC001627, BC007440, DA609383
      Related
      ENST00000383779.8

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      15560699..15601569 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      15563097..15603888 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)