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Aliases for HACL1 Gene

Aliases for HACL1 Gene

  • 2-Hydroxyacyl-CoA Lyase 1 2 3 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

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 Alpha-Methylacyl-Coa Racemase Deficiency and Beriberi. Among its related pathways are Peroxisomal lipid metabolism 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 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 , fRNAdb sequence ontologies 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
GH03I015600 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 570.9 +0.2 224 2.5 HDGF PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 HACL1 BTD CCDC174 NR2C2 SH3BP5-AS1 CAPN7 ENSG00000270409 EAF1-AS1 MRPS25 COLQ
GH03I014946 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 12.4 +653.3 653275 4.7 PKNOX1 CLOCK SMAD1 ARID4B NEUROD1 SIN3A DMAP1 ZBTB7B YY1 SLC30A9 NR2C2 FGD5-AS1 CCDC174 SH3BP5-AS1 ENSG00000228242 CAPN7 EAF1-AS1 HACL1 XPC METTL6
GH03I015323 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 11.1 +273.1 273096 11.1 HDGF PKNOX1 CLOCK FOXA2 SIN3A FEZF1 ZBTB7B IRF4 YY1 ZNF143 SH3BP5 RBSN SH3BP5-AS1 CCDC174 METTL6 NR2C2 ENSG00000270409 CAPN7 HACL1 RPS3AP53
GH03I015097 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.7 +503.0 503017 2.4 CLOCK MLX ZFP64 DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF416 GC03M015143 RBSN NR2C2 CCDC174 SH3BP5-AS1 CAPN7 ENSG00000228242 XPC MRPS25 HACL1
GH03I015205 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.7 +395.1 395079 2.7 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 CAPN7 COL6A4P1 CCDC174 SH3BP5-AS1 NR2C2 HACL1 EAF1-AS1 SH3BP5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HACL1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HACL1 gene promoter:

Genomic Locations for HACL1 Gene

Genomic Locations for HACL1 Gene
41,149 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=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for HACL1 Gene


neXtProt entry for HACL1 Gene

Post-translational modifications for HACL1 Gene

  • Ubiquitination at isoforms=2, 3, 4540

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

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 CatalyticActivity:
2-hydroxyphytanoyl-CoA = pristanal + formyl-CoA.
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.

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:0005102 receptor binding IPI 20178365
GO:0005515 protein binding IPI 16189514
GO:0016829 lyase activity IEA --
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:

Animal Model 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
plasma membrane 3
mitochondrion 1

Gene Ontology (GO) - Cellular Components for HACL1 Gene

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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HACL1 Gene

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:0006631 fatty acid metabolic process IEA --
GO:0051259 protein 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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved Nutra 0

(6) 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-CoA
  • Formyl coenzyme A
Thiamine pyrophosphate
  • Thaimine pyrophosphate
  • Thiamin diphosphate
  • Thiamin pyrophosphate
  • Thiamin-PPi
  • Thiamine diphosphate
  • (2R)-pristanal
  • (2R,6R,10R)-2,6,10,14-tetramethylpentadecanal
  • (2S)-pristanal
  • (2S,6R,10R)-2,6,10,14-tetramethylpentadecanal
  • 2(R)-Pristanal
genes like me logo Genes that share compounds with HACL1: view

Transcripts for HACL1 Gene

Unigene Clusters for HACL1 Gene

2-hydroxyacyl-CoA lyase 1:
Representative Sequences:

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
ECgene alternative splicing isoforms for

Expression for HACL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for HACL1 Gene

Protein tissue co-expression partners for HACL1 Gene

NURSA nuclear receptor signaling pathways regulating expression of HACL1 Gene:


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 33 34
  • 99.65 (n)
(Canis familiaris)
Mammalia HACL1 33 34
  • 89.68 (n)
(Bos Taurus)
Mammalia HACL1 33 34
  • 89.27 (n)
(Mus musculus)
Mammalia Hacl1 33 16 34
  • 85.7 (n)
(Rattus norvegicus)
Mammalia Hacl1 33
  • 85.58 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 75 (a)
-- 34
  • 73 (a)
-- 34
  • 69 (a)
(Monodelphis domestica)
Mammalia HACL1 34
  • 71 (a)
(Gallus gallus)
Aves HACL1 33 34
  • 73.66 (n)
(Anolis carolinensis)
Reptilia HACL1 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hacl1 33
  • 69.95 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.19375 33
(Danio rerio)
Actinopterygii hacl1 33 34
  • 65.49 (n)
wufd42e11 33
fruit fly
(Drosophila melanogaster)
Insecta CG11208 33 34
  • 55.18 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010368 33
  • 54.65 (n)
(Caenorhabditis elegans)
Secernentea CELE_B0334.3 33
  • 54.55 (n)
B0334.3 34
  • 43 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YEL020C 33
  • 50.37 (n)
-- 34
  • 39 (a)
PXP1 36
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL055C 33
  • 48.61 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G17380 33
  • 50.27 (n)
(Oryza sativa)
Liliopsida Os.15077 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC725.04 33
  • 51.75 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.11401 33
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)

Paralogs for HACL1 Gene

Paralogs for HACL1 Gene

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

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

Variants for HACL1 Gene

Sequence variations from dbSNP and Humsavar for HACL1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1057516440 likely-pathogenic, Biotinidase deficiency 15,601,895(-) G/A/C/T upstream_transcript_variant
rs1057517114 likely-pathogenic, Biotinidase deficiency 15,601,894(-) GG/G upstream_transcript_variant
rs114567021 conflicting-interpretations-of-pathogenicity, benign, Biotinidase deficiency, not specified 15,601,817(-) C/T 5_prime_UTR_variant, non_coding_transcript_variant
rs143058480 likely-pathogenic, Biotinidase deficiency 15,601,893(-) A/G/T upstream_transcript_variant
rs184480128 uncertain-significance, Biotinidase deficiency 15,601,806(-) C/G/T 5_prime_UTR_variant, non_coding_transcript_variant

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

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

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HACL1 Gene

Disorders for HACL1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for HACL1 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
alpha-methylacyl-coa racemase deficiency
  • amacrd
  • thiamine deficiency
hemangiopericytoma, malignant
  • hemangiopericytoma
- 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 22 58
  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 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. 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 58
  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 58

Products for HACL1 Gene

Sources for HACL1 Gene

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