Aliases for HACL1 Gene

Aliases for HACL1 Gene

  • 2-Hydroxyacyl-CoA Lyase 1 2 3 4 5
  • 2-Hydroxyphytanoyl-CoA Lyase 2 3 4
  • Phytanoyl-CoA 2-Hydroxylase 2 3 4
  • 2-HPCL 3 4
  • HPCL2 3 4
  • PHYH2 3 4
  • HPCL 3 4
  • 2-Hydroxyphytanol-CoA Lyase 3
  • Phytanoyl-CoA Hydroxylase 2 3
  • 1600020H07Rik 3
  • EC 4.1.-.- 4

External Ids for HACL1 Gene

Previous HGNC Symbols for HACL1 Gene

  • HPCL

Previous GeneCards Identifiers for HACL1 Gene

  • GC03M015579
  • GC03M015538
  • GC03M015602

Summaries for HACL1 Gene

GeneCards Summary for HACL1 Gene

HACL1 (2-Hydroxyacyl-CoA Lyase 1) is a Protein Coding gene. Diseases associated with HACL1 include Zellweger Syndrome and Beriberi. Among its related pathways are fatty acid alpha-oxidation III and Metabolism. Gene Ontology (GO) annotations related to this gene include identical protein binding and magnesium ion binding. An important paralog of this gene is ILVBL.

UniProtKB/Swiss-Prot Summary for HACL1 Gene

  • Catalyzes a carbon-carbon cleavage reaction; cleaves a 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde.

Additional gene information for HACL1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HACL1 Gene

Genomics for HACL1 Gene

GeneHancer (GH) Regulatory Elements for HACL1 Gene

Promoters and enhancers for HACL1 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
GH03J015600 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 510.2 +0.2 151 3 FOXK2 ZBTB40 ZNF217 CTCF ZSCAN5C SIN3A NRF1 TCF12 POLR2G SP1 HACL1 BTD ENSG00000270409 CAPN7 NR2C2 CCDC174 SH3BP5-AS1 MRPS25 COLQ
GH03J015097 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 11 +502.9 502851 2.8 FOXK2 HNRNPK ZBTB40 ZNF217 EP300 SIN3A NRF1 MYC TCF12 POLR2G RBSN lnc-NR2C2-3 piR-50437-454 CAPN7 NR2C2 CCDC174 SH3BP5-AS1 XPC ENSG00000228242 MRPS25
GH03J015557 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 13.1 +44.1 44088 0.4 CTCF REST CUX1 RAD21 SMC3 ZNF316 MAFF MAFK E2F8 ZNF654 lnc-BTD-5 piR-38516 COLQ EAF1 HACL1 ANKRD28 METTL6 SH3BP5 BTD
GH03J015561 Promoter/Enhancer 1.1 EPDnew ENCODE dbSUPER 13.1 +39.1 39060 3.5 FOXA2 JUND RXRA MAX HNF4A REST FOXA1 HNF4G ATF3 SP1 COLQ HACL1 RNU6-1024P EAF1-AS1 CAPN7 COL6A4P1 METTL6 lnc-BTD-5 BTD
GH03J015629 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 7.1 -32.6 -32635 9.5 ZNF217 CTCF TCF12 USF1 GTF2E2 JUND FOS EP300 ZIC2 REST EAF1 CAPN7 COL6A4P1 COLQ HACL1 BTD SH3BP5 ANKRD28 lnc-HACL1-2 piR-50437-456
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HACL1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HACL1

Top Transcription factor binding sites by QIAGEN in the HACL1 gene promoter:
  • AML1a
  • GR
  • GR-alpha
  • GR-beta
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • Sp1

Genomic Locations for HACL1 Gene

Genomic Locations for HACL1 Gene
41,154 bases
Minus strand
41,128 bases
Minus strand

Genomic View for HACL1 Gene

Genes around HACL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HACL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HACL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HACL1 Gene

Proteins for HACL1 Gene

  • Protein details for HACL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    2-hydroxyacyl-CoA lyase 1
    Protein Accession:
    Secondary Accessions:
    • B4DWI1
    • B4DXI5
    • E9PEN4
    • Q9BV42
    • Q9P0A2

    Protein attributes for HACL1 Gene

    578 amino acids
    Molecular mass:
    63729 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
    Quaternary structure:
    • Homotetramer.
    • Sequence=AAF28957.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for HACL1 Gene


neXtProt entry for HACL1 Gene

Post-translational modifications for HACL1 Gene

  • Ubiquitination at Lys540
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HACL1 Gene

Domains & Families for HACL1 Gene

Gene Families for HACL1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HACL1 Gene

  • Pyruvate decarboxylase
  • Thiamine pyrophosphate enzyme, C-terminal TPP-binding

Suggested Antigen Peptide Sequences for HACL1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ32415 fis, clone SKMUS2000724, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-) (B3KPX4_HUMAN)
  • cDNA FLJ53672, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-) (B4DWI1_HUMAN)
  • cDNA FLJ54118, highly similar to 2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-) (B4DXI5_HUMAN)
  • Phytanoyl-CoA 2-hydroxylase 2 (HACL1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TPP enzyme family.
  • Belongs to the TPP enzyme family.
genes like me logo Genes that share domains with HACL1: view

Function for HACL1 Gene

Molecular function for HACL1 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes a carbon-carbon cleavage reaction; cleaves a 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2-hydroxyphytanoyl-CoA = 2,6,10,14-tetramethylpentadecanal + formyl-CoA; Xref=Rhea:RHEA:25355, ChEBI:CHEBI:49189, ChEBI:CHEBI:57334, ChEBI:CHEBI:57376;.

Enzyme Numbers (IUBMB) for HACL1 Gene

Phenotypes From GWAS Catalog for HACL1 Gene

Gene Ontology (GO) - Molecular Function for HACL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000287 magnesium ion binding IEA --
GO:0003824 catalytic activity IEA --
GO:0005515 protein binding IPI 16189514
GO:0016829 lyase activity IEA --
GO:0016830 carbon-carbon lyase activity IBA,IDA 10468558
genes like me logo Genes that share ontologies with HACL1: view
genes like me logo Genes that share phenotypes with HACL1: view

Animal Models for HACL1 Gene

MGI Knock Outs for HACL1:
  • Hacl1 Hacl1<tm1b(KOMP)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for HACL1

CRISPR Products

miRNA for HACL1 Gene

miRTarBase miRNAs that target HACL1

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HACL1 Gene

Localization for HACL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HACL1 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 HACL1 gene
Compartment Confidence
peroxisome 5
nucleus 4
cytosol 4
plasma membrane 3
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HACL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005777 peroxisome IBA,IDA 10468558
GO:0005782 peroxisomal matrix TAS --
GO:0005829 cytosol TAS --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with HACL1: view

Pathways & Interactions for HACL1 Gene

genes like me logo Genes that share pathways with HACL1: view

Pathways by source for HACL1 Gene

UniProtKB/Swiss-Prot Q9UJ83-HACL1_HUMAN

  • Pathway: Lipid metabolism; fatty acid metabolism.

Gene Ontology (GO) - Biological Process for HACL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001561 fatty acid alpha-oxidation TAS,IDA --
GO:0006625 protein targeting to peroxisome TAS --
GO:0006629 lipid metabolic process IEA --
GO:0006631 fatty acid metabolic process IEA --
GO:0051259 protein complex oligomerization IDA 21708296
genes like me logo Genes that share ontologies with HACL1: view

No data available for SIGNOR curated interactions for HACL1 Gene

Drugs & Compounds for HACL1 Gene

(3) Drugs for HACL1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved, Experimental, Investigational Pharma 0
Thiamine Pyrophosphate Pharma 3

(5) Additional Compounds for HACL1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3S)-2-Hydroxyphytanoyl-CoA
  • (3S)-2-Hydroxyphytanoyl-coenzyme A
  • (3S,7R,11R)-2-Hydroxy-3,7,11,15-tetramethylhexadecanoyl-CoA
  • (3S,7R,11R)-2-Hydroxy-3,7,11,15-tetramethylhexadecanoyl-coenzyme A
  • 2-Hydroxyphytanoyl-coenzyme A
  • Formyl coenzyme A
  • Formyl-coenzyme A
  • 2,6,10,14-Tetramethylpentadecanal
  • (2R)-Pristanal
  • (2R,6R,10R)-2,6,10,14-Tetramethylpentadecanal
  • (2S)-Pristanal
  • (2S,6R,10R)-2,6,10,14-Tetramethylpentadecanal
genes like me logo Genes that share compounds with HACL1: view

Transcripts for HACL1 Gene

mRNA/cDNA for HACL1 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HACL1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^
SP1: - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - - - - - - - - - -
SP4: - - - - - -
SP5: - - - - -
SP6: - - - - -
SP7: - -
SP8: - - - -
SP9: - - - - - - -
SP10: - - - - - - - - - - -
SP11: - - - - - - -
SP12: - - -
SP13: - - - - -
SP14: - - - - - - - - - -
SP15: - - -
SP16: -
SP17: - - -
SP19: - -

ExUns: 15a · 15b ^ 16a · 16b ^ 17 ^ 18a · 18b · 18c
SP1: -
SP2: -
SP3: -

Relevant External Links for HACL1 Gene

GeneLoc Exon Structure for

Expression for HACL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HACL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HACL1 Gene

This gene is overexpressed in Testis (32.0), Liver (16.0), and Gallbladder (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HACL1 Gene

Protein tissue co-expression partners for HACL1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HACL1

SOURCE GeneReport for Unigene cluster for HACL1 Gene:


mRNA Expression by UniProt/SwissProt for HACL1 Gene:

Tissue specificity: Expressed in high levels in liver, also expressed in kidney, heart and skeletal muscle.

Evidence on tissue expression from TISSUES for HACL1 Gene

  • Liver(4.4)
  • Blood(4.3)
  • Lung(4.2)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with HACL1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HACL1 Gene

Orthologs for HACL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HACL1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HACL1 31 30
  • 99.65 (n)
(Canis familiaris)
Mammalia HACL1 31 30
  • 89.68 (n)
(Bos Taurus)
Mammalia HACL1 31 30
  • 89.27 (n)
(Mus musculus)
Mammalia Hacl1 17 31 30
  • 85.7 (n)
(Rattus norvegicus)
Mammalia Hacl1 30
  • 85.58 (n)
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 75 (a)
-- 31
  • 73 (a)
-- 31
  • 69 (a)
(Monodelphis domestica)
Mammalia HACL1 31
  • 71 (a)
(Gallus gallus)
Aves HACL1 31 30
  • 73.66 (n)
(Anolis carolinensis)
Reptilia HACL1 31
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hacl1 30
  • 69.95 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19375 30
(Danio rerio)
Actinopterygii hacl1 31 30
  • 65.49 (n)
wufd42e11 30
fruit fly
(Drosophila melanogaster)
Insecta CG11208 31 30
  • 55.18 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010368 30
  • 54.65 (n)
(Caenorhabditis elegans)
Secernentea CELE_B0334.3 30
  • 54.55 (n)
B0334.3 31
  • 43 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YEL020C 30
  • 50.37 (n)
-- 31
  • 39 (a)
PXP1 33
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL055C 30
  • 48.61 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G17380 30
  • 50.27 (n)
(Oryza sativa)
Liliopsida Os.15077 30
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 55 (a)
Cin.11401 30
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC725.04 30
  • 51.75 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11401 30
Species where no ortholog for HACL1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HACL1 Gene

Gene Tree for HACL1 (if available)
Gene Tree for HACL1 (if available)
Evolutionary constrained regions (ECRs) for HACL1: view image

Paralogs for HACL1 Gene

Paralogs for HACL1 Gene

(2) SIMAP similar genes for HACL1 Gene using alignment to 8 proteins:

  • C9J306_HUMAN
  • Q7Z773_HUMAN
genes like me logo Genes that share paralogs with HACL1: view

Variants for HACL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HACL1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
767887 Benign: not provided 15,582,929(-) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
780104 Benign: not provided 15,573,200(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for HACL1 Gene

Structural Variations from Database of Genomic Variants (DGV) for HACL1 Gene

Variant ID Type Subtype PubMed ID
esv2228566 CNV deletion 18987734
esv2724966 CNV deletion 23290073
esv2724967 CNV deletion 23290073
nsv834622 CNV gain 17160897

Variation tolerance for HACL1 Gene

Residual Variation Intolerance Score: 41.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.26; 52.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HACL1 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 HACL1 Gene

Disorders for HACL1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for HACL1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
zellweger syndrome
  • zs
  • thiamine deficiency
- elite association - COSMIC cancer census association via MalaCards
Search HACL1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HACL1

genes like me logo Genes that share disorders with HACL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HACL1 Gene

Publications for HACL1 Gene

  1. Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during alpha-oxidation of 3-methyl-branched fatty acids. (PMID: 10468558) Foulon V … Casteels M (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4 23 54
  2. Breakdown of 2-hydroxylated straight chain fatty acids via peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the alpha-oxidation of straight chain fatty acids. (PMID: 15644336) Foulon V … Casteels M (The Journal of biological chemistry 2005) 2 3 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PMID: 11042152) Zhang QH … Chen Z (Genome research 2000) 3 4 54

Products for HACL1 Gene

Sources for HACL1 Gene