HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
HLCS
holocarboxylase synthetase
Chromosome 21 · 21q22.13
NCBI Gene: 3141Ensembl: ENSG00000159267HGNC: HGNC:4976UniProt: A0A8C8QSB1
72PubMed Papers
21Diseases
0Drugs
194Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
biotin--[biotin carboxyl-carrier protein] ligase activityprotein bindingbiotin bindingenzyme bindingholocarboxylase synthetase deficiencyvitamin metabolic disordergenetic disorderneurodegenerative disease
✦AI Summary

HLCS (holocarboxylase synthetase) is a biotin–protein ligase that catalyzes the covalent attachment of biotin to four biotin-dependent carboxylases: acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, and methylcrotonyl-CoA carboxylase 1. These carboxylases are essential enzymes involved in cellular metabolism of fatty acids and amino acids, and gluconeogenesis 2. HLCS also biotinylates histones, linking biotin metabolism to gene regulation 1. Biotin, a water-soluble B-vitamin cofactor, is not synthesized endogenously and must be obtained from dietary sources or intestinal bacterial production 2. HLCS deficiency is an autosomal recessive disorder characterized by defective biotin incorporation into carboxylases, leading to impaired enzyme function 1. Clinical manifestations include neurological and dermatological symptoms, with disease severity correlating with residual HLCS enzyme activity 1. Patients with mutations producing minimal residual activity present with neonatal onset, while those with higher residual activity develop later-onset symptoms 1. High-dose biotin therapy shows clinical efficacy in HLCS deficiency patients 2, with responsiveness directly related to preserved enzyme function 1. Over 30 HLCS mutations have been identified, distributed across the coding region, including population-specific founder mutations in Scandinavian and Japanese populations 1.

Sources cited
1
HLCS catalyzes biotin incorporation into carboxylases and histones; deficiency is autosomal recessive; describes 30+ mutations with clinical-phenotype correlations and biotin responsiveness
PMID: 16134170
2
Biotin functions as cofactor for carboxylases in fatty acid/amino acid metabolism and gluconeogenesis; biotin obtained from diet/intestinal bacteria; high-dose biotin treatment for HLCS deficiency
PMID: 38928282
⚠Limited data available — This gene has 2 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ21
holocarboxylase synthetase deficiencyOpen Targets
0.86Strong
vitamin metabolic disorderOpen Targets
0.53Moderate
genetic disorderOpen Targets
0.47Moderate
neurodegenerative diseaseOpen Targets
0.38Weak
male infertilityOpen Targets
0.30Weak
bronchopneumoniaOpen Targets
0.23Weak
exostosisOpen Targets
0.23Weak
Lung AbscessOpen Targets
0.23Weak
familial isolated deficiency of vitamin EOpen Targets
0.12Weak
HirsutismOpen Targets
0.08Suggestive
neoplasmOpen Targets
0.08Suggestive
hypoparathyroidism, familial isolated, 2Open Targets
0.06Suggestive
Familial isolated hypoparathyroidismOpen Targets
0.06Suggestive
Griscelli diseaseOpen Targets
0.06Suggestive
pseudohypoparathyroidism type 2Open Targets
0.06Suggestive
intestinal hypomagnesemia 1Open Targets
0.05Suggestive
Primary hypomagnesemia with secondary hypocalcemiaOpen Targets
0.05Suggestive
Griscelli disease type 3Open Targets
0.05Suggestive
Griscelli syndrome type 3Open Targets
0.05Suggestive
Abnormality of the skeletal systemOpen Targets
0.05Suggestive
Holocarboxylase synthetase deficiencyUniProt
Pathogenic Variants194
NM_001352514.2(HLCS):c.1096dup (p.Ile366fs)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2026→ Residue 366
NM_001352514.2(HLCS):c.2237-2A>GLikely pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2026
NM_001352514.2(HLCS):c.1963C>T (p.Arg655Trp)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2026→ Residue 655
NM_001352514.2(HLCS):c.2450+2T>ALikely pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2026
NM_001352514.2(HLCS):c.1974dup (p.Val659fs)Pathogenic
Holocarboxylase synthetase deficiency|not provided|Inborn genetic diseases
★★☆☆2026→ Residue 659
NM_001352514.2(HLCS):c.2089G>A (p.Val697Met)Pathogenic
Holocarboxylase synthetase deficiency|not provided
★★☆☆2026→ Residue 697
NM_001352514.2(HLCS):c.1434C>A (p.Cys478Ter)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2026→ Residue 478
NM_001352514.2(HLCS):c.1083T>A (p.Cys361Ter)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2026→ Residue 361
NM_001352514.2(HLCS):c.1960+5G>APathogenic
Holocarboxylase synthetase deficiency|not provided|Ovarian serous cystadenocarcinoma
★★☆☆2025
NM_001352514.2(HLCS):c.569_585delinsTTGCTTGAGATTAAGCCTGAGATTAAGG (p.Pro190_Ser195delinsLeuAlaTer)Likely pathogenic
not provided|Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 190
NM_001352514.2(HLCS):c.2152G>A (p.Asp718Asn)Pathogenic
Holocarboxylase synthetase deficiency|not provided
★★☆☆2025→ Residue 718
NM_001352514.2(HLCS):c.958C>T (p.Gln320Ter)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 320
NM_001352514.2(HLCS):c.1769dup (p.Met590fs)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 590
NM_001352514.2(HLCS):c.2434C>T (p.Arg812Ter)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 812
NM_001352514.2(HLCS):c.2182G>A (p.Gly728Ser)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 728
NM_001352514.2(HLCS):c.331-1G>CLikely pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025
NM_001352514.2(HLCS):c.1658_1659del (p.His553fs)Pathogenic
Holocarboxylase synthetase deficiency|not provided
★★☆☆2025→ Residue 553
NM_001352514.2(HLCS):c.1045G>T (p.Glu349Ter)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 349
NM_001352514.2(HLCS):c.664C>T (p.Gln222Ter)Pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 222
NM_001352514.2(HLCS):c.1162G>T (p.Gly388Trp)Likely pathogenic
Holocarboxylase synthetase deficiency
★★☆☆2025→ Residue 388
View on ClinVar ↗
Related Genes
FN3KRPShared pathway100%MCCC2Protein interaction100%PCCBProtein interaction100%ACACAProtein interaction98%BTDProtein interaction98%MCCC1Protein interaction98%
Tissue Expression6 tissues
Brain
100%
Liver
98%
Heart
47%
Lung
41%
Ovary
30%
Bone Marrow
18%
Gene Interaction Network
Click a node to explore
HLCSFN3KRPMCCC2PCCBACACABTDMCCC1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt P50747
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.88LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.69 [0.55–0.88]
RankingsWhere HLCS stands among ~20K protein-coding genes
  • #6,550of 20,598
    Most Researched72
  • #360of 5,498
    Most Pathogenic Variants194 · top 10%
  • #7,865of 17,882
    Most Constrained (LOEUF)0.88
Genes detectedHLCS
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Biotin Homeostasis and Human Disorders: Recent Findings and Perspectives.
PMID: 38928282
Int J Mol Sci · 2024
1.00
2
Mutations in the holocarboxylase synthetase gene HLCS.
PMID: 16134170
Hum Mutat · 2005
0.90
3
Stem cell-derived polarized hepatocytes.
PMID: 32245952
Nat Commun · 2020
0.80
4
Innate immunity in stem cell-derived hepatocytes.
PMID: 29786555
Philos Trans R Soc Lond B Biol Sci · 2018
0.70
5
CircRNA HLCS regulates lens epithelial cell apoptosis via miR-338-3p/BPNT1 axis.
PMID: 38493427
Int Ophthalmol · 2024
0.60