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Aliases for HLCS Gene

Aliases for HLCS Gene

  • Holocarboxylase Synthetase (Biotin-(Proprionyl-CoA-Carboxylase (ATP-Hydrolysing)) Ligase) 2 3
  • Holocarboxylase Synthetase (Biotin-(Proprionyl-Coenzyme A-Carboxylase (ATP-Hydrolysing)) Ligase) 2 3
  • Biotin Apo-Protein Ligase 3 4
  • HCS 3 6
  • Holocarboxylase Synthetase (Biotin-[Proprionyl-Coenzyme A-Carboxylase (ATP-Hydrolysing)] Ligase) 2
  • Biotin--[Methylmalonyl-CoA-Carboxytransferase] Ligase 3
  • Biotin--[Methylcrotonoyl-CoA-Carboxylase] Ligase 3
  • Biotin--[Acetyl-CoA-Carboxylase] Ligase 3
  • Biotin--Protein Ligase 3
  • EC 6.3.4.- 4

External Ids for HLCS Gene

Previous GeneCards Identifiers for HLCS Gene

  • GC21M034700
  • GC21M037043
  • GC21M037045
  • GC21M038123
  • GC21M023599

Summaries for HLCS Gene

Entrez Gene Summary for HLCS Gene

  • This gene encodes an enzyme that catalyzes the binding of biotin to carboxylases and histones. The protein plays an important role in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. Defects in this gene are the cause of holocarboxylase synthetase deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jun 2011]

GeneCards Summary for HLCS Gene

HLCS (Holocarboxylase Synthetase (Biotin-(Proprionyl-CoA-Carboxylase (ATP-Hydrolysing)) Ligase)) is a Protein Coding gene. Diseases associated with HLCS include holocarboxylase synthetase deficiency and biotinidase deficiency. Among its related pathways are Disease and Metabolism. GO annotations related to this gene include protein homodimerization activity and biotin binding.

UniProtKB/Swiss-Prot for HLCS Gene

  • Post-translational modification of specific protein by attachment of biotin. Acts on various carboxylases such as acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl CoA carboxylase, and 3-methylcrotonyl CoA carboxylase

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HLCS Gene

Genomics for HLCS Gene

Regulatory Elements for HLCS Gene

Genomic Location for HLCS Gene

Start:
36,750,888 bp from pter
End:
36,990,245 bp from pter
Size:
239,358 bases
Orientation:
Minus strand

Genomic View for HLCS Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for HLCS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HLCS Gene

Proteins for HLCS Gene

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

    Protein Symbol:
    P50747-BPL1_HUMAN
    Recommended name:
    Biotin--protein ligase
    Protein Accession:
    P50747
    Secondary Accessions:
    • B2RAH1
    • D3DSG6
    • Q99451

    Protein attributes for HLCS Gene

    Size:
    726 amino acids
    Molecular mass:
    80760 Da
    Quaternary structure:
    • Monomer
    SequenceCaution:
    • Sequence=AK307940; Type=Frameshift; Positions=169; Evidence={ECO:0000305};

neXtProt entry for HLCS Gene

Proteomics data for HLCS Gene at MOPED

Post-translational modifications for HLCS Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HLCS Gene

No data available for DME Specific Peptides for HLCS Gene

Domains for HLCS Gene

Protein Domains for HLCS Gene

Suggested Antigen Peptide Sequences for HLCS Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P50747

UniProtKB/Swiss-Prot:

BPL1_HUMAN :
  • P50747
Domain:
  • Contains 1 BPL/LPL catalytic domain.
Family:
  • Belongs to the biotin--protein ligase family.
genes like me logo Genes that share domains with HLCS: view

No data available for Gene Families for HLCS Gene

Function for HLCS Gene

Molecular function for HLCS Gene

GENATLAS Biochemistry: holocarboxylase synthetase,80kDa,cytosolic,with two alternatively spliced isoforms,catalyzing the biotinylation of the four biotin-dependent carboxylases,including the mitochondrial pyruvate carboxylase,propionyl-CoA carboxylase,methylcrotonyl-CoA carboxylase and the cytosolic acetyl-CoA carboxylase
UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=224 nM for biotin {ECO:0000269 PubMed:10590022}; Vmax=143.9 pmol/min/mg enzyme {ECO:0000269 PubMed:10590022};
UniProtKB/Swiss-Prot CatalyticActivity: ATP + biotin + apo-[methylmalonyl-CoA:pyruvate carboxytransferase] = AMP + diphosphate + [methylmalonyl-CoA:pyruvate carboxytransferase]
UniProtKB/Swiss-Prot CatalyticActivity: ATP + biotin + apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [propionyl-CoA:carbon-dioxide ligase (ADP-forming)]
UniProtKB/Swiss-Prot CatalyticActivity: ATP + biotin + apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)]
UniProtKB/Swiss-Prot CatalyticActivity: ATP + biotin + apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [acetyl-CoA:carbon-dioxide ligase (ADP-forming)]
UniProtKB/Swiss-Prot Function: Post-translational modification of specific protein by attachment of biotin. Acts on various carboxylases such as acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl CoA carboxylase, and 3-methylcrotonyl CoA carboxylase

Enzyme Numbers (IUBMB) for HLCS Gene

Gene Ontology (GO) - Molecular Function for HLCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004077 biotin-[acetyl-CoA-carboxylase] ligase activity IEA --
GO:0004078 biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity IEA --
GO:0004079 biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity IEA --
GO:0004080 biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity IDA 7842009
GO:0005515 protein binding IPI 20085763
genes like me logo Genes that share ontologies with HLCS: view

No data available for Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for HLCS Gene

Localization for HLCS Gene

Subcellular locations from UniProtKB/Swiss-Prot for HLCS Gene

Cytoplasm. Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HLCS Gene COMPARTMENTS Subcellular localization image for HLCS gene
Compartment Confidence
cytosol 5
mitochondrion 5
nucleus 5
endoplasmic reticulum 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for HLCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 14613969
GO:0005652 nuclear lamina IDA 14613969
GO:0005737 cytoplasm IDA --
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with HLCS: view

Pathways for HLCS Gene

SuperPathways for HLCS Gene

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

Gene Ontology (GO) - Biological Process for HLCS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006464 cellular protein modification process --
GO:0006766 vitamin metabolic process TAS --
GO:0006767 water-soluble vitamin metabolic process TAS --
GO:0006768 biotin metabolic process TAS --
GO:0008283 cell proliferation IMP 18429047
genes like me logo Genes that share ontologies with HLCS: view

Compounds for HLCS Gene

(6) HMDB Compounds for HLCS Gene

Compound Synonyms Cas Number PubMed IDs
Adenosine monophosphate
  • 5'-AMP
61-19-8
Adenosine triphosphate
  • 5'-(tetrahydrogen triphosphate) Adenosine
56-65-5
Biotin
  • (+)-Biotin
58-85-5
Biotinyl-5'-AMP
  • (+)-Biotinyl 5'-adenylate
4130-20-5
Phosphoric acid
  • acide phosphorique (FRENCH)
7664-38-2

(1) Drugbank Compounds for HLCS Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Biotin
  • (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid
58-85-5 target

(17) Novoseek inferred chemical compound relationships for HLCS Gene

Compound -log(P) Hits PubMed IDs
biotin 93.9 159
3-methylcrotonyl-coa 79.5 2
multivitamin 67 2
d-biotin 66.3 1
acetyl-coa 63.6 5
genes like me logo Genes that share compounds with HLCS: view

Transcripts for HLCS Gene

Unigene Clusters for HLCS Gene

Holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase):
Representative Sequences:

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

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e · 10f · 10g · 10h ^ 11a ·
SP1: - - - - - - - - - -
SP2: -
SP3: - - - - - - - - -
SP4: - - - - -
SP5: - - - - - - - - - -
SP6: - - - - - - -
SP7: - - - - -
SP8: - -
SP9: - - -
SP10: - - - - - - - - - - -
SP11: - - - - - - - - - - - -
SP12: - - - - - -
SP13:
SP14:
SP15:

ExUns: 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20
SP1: - - - -
SP2: - - - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for HLCS Gene

GeneLoc Exon Structure for
HLCS
ECgene alternative splicing isoforms for
HLCS

Expression for HLCS Gene

mRNA expression in normal human tissues for HLCS Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HLCS Gene

SOURCE GeneReport for Unigene cluster for HLCS Gene Hs.371350

mRNA Expression by UniProt/SwissProt for HLCS Gene

P50747-BPL1_HUMAN
Tissue specificity: Mostly expressed in muscle, placenta, in lesser extent in the brain, kidney, pancreas, liver and lung
genes like me logo Genes that share expressions with HLCS: view

No data available for mRNA differential expression in normal tissues for HLCS Gene

Orthologs for HLCS Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HLCS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HLCS 35
  • 99.27 (n)
  • 99.17 (a)
HLCS 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia HLCS 35
  • 80.07 (n)
  • 75.59 (a)
HLCS 36
  • 73 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HLCS 35
  • 82.02 (n)
  • 79.53 (a)
HLCS 36
  • 79 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hlcs 35
  • 78.59 (n)
  • 77.25 (a)
Hlcs 16
Hlcs 36
  • 77 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HLCS 36
  • 54 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HLCS 36
  • 50 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hlcs 35
  • 78.64 (n)
  • 77.39 (a)
chicken
(Gallus gallus)
Aves HLCS 35
  • 64.57 (n)
  • 61.12 (a)
HLCS 36
  • 50 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HLCS 36
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hlcs 35
  • 60.84 (n)
  • 56.94 (a)
zebrafish
(Danio rerio)
Actinopterygii Dr.12060 35
hlcs 35
  • 51.5 (n)
  • 43.13 (a)
hlcs 36
  • 29 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Hcs 36
  • 16 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea bpl-1 35
  • 42.72 (n)
  • 30.71 (a)
bpl-1 36
  • 11 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BPL1 36
  • 20 (a)
OneToOne
BPL1 38
thale cress
(Arabidopsis thaliana)
eudicotyledons HCS1 35
  • 46.01 (n)
  • 34.22 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 44 (a)
OneToOne
Species with no ortholog for HLCS:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HLCS Gene

ENSEMBL:
Gene Tree for HLCS (if available)
TreeFam:
Gene Tree for HLCS (if available)

Paralogs for HLCS Gene

No data available for Paralogs for HLCS Gene

Variants for HLCS Gene

Sequence variations from dbSNP and Humsavar for HLCS Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type MAF
rs14407 -- 36,751,624(-) AAATC(A/G)TGGTT utr-variant-3-prime, downstream-variant-500B
rs28530 -- 36,979,922(+) tggtg(C/G)tgtgt intron-variant
rs369888 -- 36,956,022(+) ctaga(C/T)ttgta intron-variant
rs381712 -- 36,989,620(+) caccg(C/T)gcccg intron-variant
rs391554 -- 36,983,785(+) TGAGA(C/T)GAGAT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv913735 CNV Loss 21882294
nsv913736 CNV Loss 21882294
nsv3507 CNV Loss 18451855
esv2676526 CNV Deletion 23128226
nsv498978 CNV Loss 21111241
esv26519 CNV Loss 19812545
esv2751929 CNV Gain 17911159
esv2659201 CNV Deletion 23128226
nsv510504 CNV Loss 20534489
nsv3508 CNV Insertion 18451855
esv2666311 CNV Deletion 23128226

Relevant External Links for HLCS Gene

HapMap Linkage Disequilibrium report
HLCS
Human Gene Mutation Database (HGMD)
HLCS

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

Disorders for HLCS Gene

(1) OMIM Diseases for HLCS Gene (609018)

UniProtKB/Swiss-Prot

BPL1_HUMAN
  • Holocarboxylase synthetase deficiency (HLCS deficiency) [MIM:253270]: A neonatal form of multiple carboxylase deficiency, an autosomal recessive disorder of biotin metabolism, characterized by ketoacidosis, hyperammonemia, excretion of abnormal organic acid metabolites, and dermatitis. In holocarboxylase synthetase deficiency, clinical and biochemical symptoms improve dramatically with administration of biotin. {ECO:0000269 PubMed:10190325, ECO:0000269 PubMed:10590022, ECO:0000269 PubMed:11735028, ECO:0000269 PubMed:12124727, ECO:0000269 PubMed:12633764, ECO:0000269 PubMed:16134170, ECO:0000269 PubMed:20095979, ECO:0000269 PubMed:25690727, ECO:0000269 PubMed:7842009, ECO:0000269 PubMed:8541348, ECO:0000269 PubMed:8817339, ECO:0000269 PubMed:9396568}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for HLCS Gene

(16) Novoseek inferred disease relationships for HLCS Gene

Disease -log(P) Hits PubMed IDs
holocarboxylase synthetase deficiency 99.1 52
multiple carboxylase deficiency 98.7 26
biotinidase deficiency 91.4 13
aciduria organic 81.5 2
metabolic acidosis 64.6 4

Genatlas disease for HLCS Gene

multiple carboxylase deficiency,early onset with feeding difficulties,hypotonia,seizures,lethargy and metabolic acidosis mild,hyperammonemia,organic aciduria

Relevant External Links for HLCS

Genetic Association Database (GAD)
HLCS
genes like me logo Genes that share disorders with HLCS: view

Publications for HLCS Gene

  1. Isolation and characterization of mutations in the human holocarboxylase synthetase cDNA. (PMID: 7842009) Suzuki Y. … Narisawa K. (Nat. Genet. 1994) 2 3 4 23
  2. Molecular analysis of holocarboxylase synthetase deficiency: a missense mutation and a single base deletion are predominant in Japanese patients. (PMID: 8541348) Aoki Y. … Narisawa K. (Biochim. Biophys. Acta 1995) 3 4 23
  3. Gene identification in 1.6-Mb region of the Down syndrome region on chromosome 21. (PMID: 9037601) Ohira M. … Ohki M. (Genome Res. 1997) 3 4 23
  4. Clustering of mutations in the biotin-binding region of holocarboxylase synthetase in biotin-responsive multiple carboxylase deficiency. (PMID: 8817339) Dupuis L. … Gravel R.A. (Hum. Mol. Genet. 1996) 3 4 23
  5. Characterization of mutant holocarboxylase synthetase (HCS): a Km for biotin was not elevated in a patient with HCS deficiency. (PMID: 9396568) Aoki Y. … Narisawa K. (Pediatr. Res. 1997) 3 4 23

Products for HLCS Gene

Sources for HLCS Gene

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