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HLCS holocarboxylase synthetase [ Homo sapiens (human) ]

Gene ID: 3141, updated on 3-Apr-2024

Summary

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Official Symbol
HLCSprovided by HGNC
Official Full Name
holocarboxylase synthetaseprovided by HGNC
Primary source
HGNC:HGNC:4976
See related
Ensembl:ENSG00000159267 MIM:609018; AllianceGenome:HGNC:4976
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
HCS
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 4.3), prostate (RPKM 3.3) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See HLCS in Genome Data Viewer
Location:
21q22.13
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (36748625..36990211, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35130819..35372426, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38120926..38362511, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38031419-38031920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38031921-38032420 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr21:38067894-38068806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38072642-38073235 Neighboring gene uncharacterized LOC107985492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38073236-38073828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38077313-38078142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38078973-38079802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38081463-38082292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38091813-38092599 Neighboring gene SIM bHLH transcription factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13289 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:38121986-38122511 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:38122512-38123036 Neighboring gene NANOG hESC enhancer GRCh37_chr21:38128709-38129210 Neighboring gene uncharacterized LOC105369305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38158985-38159520 Neighboring gene Sharpr-MPRA regulatory region 9348 Neighboring gene HLCS intron CAGE-defined mid-level expression enhancer Neighboring gene RNA, 5S ribosomal pseudogene 491 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:38281839-38283038 Neighboring gene Sharpr-MPRA regulatory region 2954 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:38300053-38300245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38312167-38312666 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:38319174-38319727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18441 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:38338431-38338761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13291 Neighboring gene divergent-paired related homeobox pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13292 Neighboring gene HLCS antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13293 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38378343-38378843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18442 Neighboring gene mitochondrial ribosomal protein L20 pseudogene 1 Neighboring gene ripply transcriptional repressor 3

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
  • 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. Holocarboxylase Synthetase: A Moonlighting Transcriptional Coregulator of Gene Expression and a Cytosolic Regulator of Biotin Utilization. León-Del-Río A, et al. Annu Rev Nutr, 2017 Aug 21. PMID 28564555
  2. Three promoters regulate the transcriptional activity of the human holocarboxylase synthetase gene. Xia M, et al. J Nutr Biochem, 2013 Nov. PMID 24075901, Free PMC Article
  3. Effects of single-nucleotide polymorphisms in the human holocarboxylase synthetase gene on enzyme catalysis. Esaki S, et al. Eur J Hum Genet, 2012 Apr. PMID 22027809, Free PMC Article
  4. Human holocarboxylase synthetase with a start site at methionine-58 is the predominant nuclear variant of this protein and has catalytic activity. Bao B, et al. Biochem Biophys Res Commun, 2011 Aug 19. PMID 21802411, Free PMC Article
  5. Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate biotinylation of K9 and K18. Bao B, et al. J Nutr Biochem, 2011 May. PMID 20688500, Free PMC Article

See all (64) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircRNA HLCS regulates lens epithelial cell apoptosis via miR-338-3p/BPNT1 axis.
    Title: CircRNA HLCS regulates lens epithelial cell apoptosis via miR-338-3p/BPNT1 axis.
  2. Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation.
    Title: Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation.
  3. Clinical, biochemical, and genetic analysis of 28 Chinese patients with holocarboxylase synthetase deficiency.
    Title: Clinical, biochemical, and genetic analysis of 28 Chinese patients with holocarboxylase synthetase deficiency.
  4. The function of HCS and biotin in metabolism and human disease, a putative role for the enzyme in histone biotinylation, and its participation as a nuclear factor in chromatin dynamics is discussed.
    Title: Holocarboxylase Synthetase: A Moonlighting Transcriptional Coregulator of Gene Expression and a Cytosolic Regulator of Biotin Utilization.
  5. The transcriptional function of HCS was shown by in vitro pull down and in vivo co-immunoprecipitation assays to depend on its interaction with the histone deacetylases HDAC1, HDAC2 and HDAC7
    Title: Holocarboxylase synthetase acts as a biotin-independent transcriptional repressor interacting with HDAC1, HDAC2 and HDAC7.
  6. Data suggest that direct interactions of HLCS (holocarboxylase synthetase) with NCOR1 (nuclear receptor corepressor 1) and HDAC1 (histone deacetylase 1) contribute toward transcriptional repression of repeats, presumably increasing genome stability.
    Title: Holocarboxylase synthetase interacts physically with nuclear receptor co-repressor, histone deacetylase 1 and a novel splicing variant of histone deacetylase 1 to repress repeats.
  7. study characterizes three functional promoters in the human HLCS gene
    Title: Three promoters regulate the transcriptional activity of the human holocarboxylase synthetase gene.
  8. HLCS interacts physically with the DNA methyltransferase DNMT1 and the methyl CpG binding protein MeCP2 to facilitate the binding of HLCS to chromatin.
    Title: Holocarboxylase synthetase synergizes with methyl CpG binding protein 2 and DNA methyltransferase 1 in the transcriptional repression of long-terminal repeats.
  9. This study showed that modification of HSP72 and demonstrated that binding of biotin to extracellular HSP72 prepares cells for a strong immune response.
    Title: Holocarboxylase synthetase catalyzes biotinylation of heat shock protein 72, thereby inducing RANTES expression in HEK-293 cells.
  10. individuals with HLCS SNPs may benefit from supplemental biotin, yet to different extents depending on the genotype
    Title: Effects of single-nucleotide polymorphisms in the human holocarboxylase synthetase gene on enzyme catalysis.
Submit: New GeneRIF Correction See all GeneRIFs (28)

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
Holocarboxylase synthetase deficiency
MedGen: C0268581 OMIM: 253270 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 ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables biotin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables biotin-[acetyl-CoA-carboxylase] ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables biotin-protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables biotin-protein ligase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables biotin-protein ligase activity TAS
Traceable Author Statement
more info
  
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biotin metabolic process TAS
Traceable Author Statement
more info
  
involved_in post-translational protein modification IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to biotin IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol HDA PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear lamina IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear matrix IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
biotin--protein ligase
Names
biotin apo-protein ligase
biotin--[acetyl-CoA-carboxylase] ligase
biotin--[methylcrotonoyl-CoA-carboxylase] ligase
biotin--[methylmalonyl-CoA-carboxytransferase] ligase
holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)
holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)
NP_000402.3
NP_001229713.1
NP_001229714.1
NP_001339443.1
NP_001339444.1
NP_001339445.1
NP_001339446.1
NP_001339447.1
XP_011527842.1
XP_024307833.1
XP_047296708.1
XP_047296709.1
XP_047296710.1
XP_047296711.1
XP_047296712.1
XP_054180425.1
XP_054180426.1
XP_054180427.1
XP_054180428.1
XP_054180429.1
XP_054180430.1
XP_054180431.1

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_016193.2 RefSeqGene

    Range
    28726..246769
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000411.8 → NP_000402.3  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_000402.3

    Status: REVIEWED

    Source sequence(s)
    AP000697, D23672, D87328
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451
    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Related
    ENSP00000338387.3, ENST00000336648.8
    Conserved Domains (3) summary
    pfam02237
    Location:669 → 716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467 → 647
    BPL; biotin protein ligase
    cl00020
    Location:202 → 460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  2. NM_001242784.3 → NP_001229713.1  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_001229713.1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000704, D87328, DB290499
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451
    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Related
    ENSP00000382071.1, ENST00000399120.5
    Conserved Domains (3) summary
    pfam02237
    Location:669 → 716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467 → 647
    BPL; biotin protein ligase
    cl00020
    Location:202 → 460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  3. NM_001242785.2 → NP_001229714.1  biotin--protein ligase isoform 1

    See identical proteins and their annotated locations for NP_001229714.1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451
    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Related
    ENSP00000479939.1, ENST00000612277.4
    Conserved Domains (3) summary
    pfam02237
    Location:669 → 716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467 → 647
    BPL; biotin protein ligase
    cl00020
    Location:202 → 460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  4. NM_001352514.2 → NP_001339443.1  biotin--protein ligase isoform 2

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS93094.1
    UniProtKB/TrEMBL
    A0A8C8QSB1
    Related
    ENSP00000502087.2, ENST00000674895.3
    Conserved Domains (3) summary
    pfam02237
    Location:816 → 863
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:614 → 794
    BPL; biotin protein ligase
    cl00020
    Location:349 → 607
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  5. NM_001352515.2 → NP_001339444.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451
    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Related
    ENSP00000501832.1, ENST00000675057.1
    Conserved Domains (3) summary
    pfam02237
    Location:669 → 716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467 → 647
    BPL; biotin protein ligase
    cl00020
    Location:202 → 460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  6. NM_001352516.2 → NP_001339445.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451
    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Related
    ENSP00000501750.1, ENST00000675307.1
    Conserved Domains (3) summary
    pfam02237
    Location:669 → 716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467 → 647
    BPL; biotin protein ligase
    cl00020
    Location:202 → 460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  7. NM_001352517.1 → NP_001339446.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451
    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Conserved Domains (3) summary
    pfam02237
    Location:669 → 716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467 → 647
    BPL; biotin protein ligase
    cl00020
    Location:202 → 460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  8. NM_001352518.2 → NP_001339447.1  biotin--protein ligase isoform 1

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704
    Consensus CDS
    CCDS13647.1
    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451
    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Conserved Domains (3) summary
    pfam02237
    Location:669 → 716
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:467 → 647
    BPL; biotin protein ligase
    cl00020
    Location:202 → 460
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

RNA

  1. NR_148020.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704

  2. NR_148021.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP000697, AP000698, AP000702, AP000703, AP000704

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    36748625..36990211 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452065.2 → XP_024307833.1  biotin--protein ligase isoform X4

    UniProtKB/TrEMBL
    A0A6Q8PFK4
    Conserved Domains (3) summary
    pfam02237
    Location:612 → 659
    BPL_C; Biotin protein ligase C terminal domain
    cd16442
    Location:410 → 590
    BPL; biotin protein ligase
    cl00020
    Location:145 → 403
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  2. XM_047440752.1 → XP_047296708.1  biotin--protein ligase isoform X1

  3. XM_047440754.1 → XP_047296710.1  biotin--protein ligase isoform X3

    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451

  4. XM_047440753.1 → XP_047296709.1  biotin--protein ligase isoform X2

  5. XM_047440756.1 → XP_047296712.1  biotin--protein ligase isoform X7

  6. XM_011529540.3 → XP_011527842.1  biotin--protein ligase isoform X5

    Conserved Domains (1) summary
    cl00020
    Location:349 → 607
    GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

  7. XM_047440755.1 → XP_047296711.1  biotin--protein ligase isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    35130819..35372426 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324453.1 → XP_054180428.1  biotin--protein ligase isoform X4

  2. XM_054324450.1 → XP_054180425.1  biotin--protein ligase isoform X1

  3. XM_054324452.1 → XP_054180427.1  biotin--protein ligase isoform X3

    UniProtKB/Swiss-Prot
    B2RAH1, D3DSG6, P50747, Q99451

  4. XM_054324451.1 → XP_054180426.1  biotin--protein ligase isoform X2

  5. XM_054324456.1 → XP_054180431.1  biotin--protein ligase isoform X7

  6. XM_054324454.1 → XP_054180429.1  biotin--protein ligase isoform X5

  7. XM_054324455.1 → XP_054180430.1  biotin--protein ligase isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P50747.1 GenPept UniProtKB/Swiss-Prot:P50747

Gene LinkOut

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