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Gene

HLCS

holocarboxylase synthetase

Summary

Cytogenetic location
21q22.13
Coordinates
Chromosome 21: 36,748,626–36,966,669 (GRCh38)
Exons
11 exons across 218 kb
Protein
873 amino acids
Inheritance
Autosomal recessive
Also known as
HCS
MANE Select transcript
ENST00000674895.3NM_001352514.2
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Biotinidase & Holocarboxylase Deficiency

    • Biotinidase and Holocarboxylase Synthetase Deficiency (Multiple Carboxylase Deficiency)Autosomal recessive

      Caused by variants in BTD or HLCS, these conditions can lead to seizures, skin rash, hair loss, hearing and vision loss and metabolic crises if untreated; some BTD variants cause only partial enzyme deficiency, which is usually mild.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing allows inexpensive lifelong biotin treatment, which can prevent the serious neurological and metabolic effects of profound deficiency.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How HLCS is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 21, with a bracket where HLCS sits. HLCS and 8 genes near it on chromosome 21, from 36,357,648 to 37,357,647.Chromosome 2121q22.13p13p12p11.2p11.1q11.1q11.2q21.1q21.2q21.3q22.11q22.12q22.13q22.2q22.336.4 Mb36.6 Mb36.8 Mb37 Mb37.2 MbMORC3: 36,320,180–36,386,148, forward strandMORC3CHAF1B: 36,385,354–36,419,015, forward strandCHAF1BCLDN14: 36,460,616–36,576,569, reverse strandCLDN14SIM2: 36,699,104–36,751,135, forward strandSIM2HLCS: 36,748,626–36,966,669, reverse strandHLCSRIPPLY3: 37,006,150–37,019,662, forward strandRIPPLY3PIGP: 37,036,533–37,073,820, reverse strandPIGPTTC3: 37,073,206–37,203,112, forward strandTTC3VPS26C: 37,221,749–37,268,104, reverse strandVPS26CDiagram of HLCS: 11 exons on the reverse strand of chromosome 21Exon 11: 3 known disease-causing sitesExon 10: 13 known disease-causing sitesExon 9: 11 known disease-causing sitesExon 8: 15 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 6: 27 known disease-causing sitesExon 5: 25 known disease-causing sitesExon 4: 77 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 11: 36,748,626–36,754,417, 5,792 basesExon 10: 36,756,542–36,756,755, 214 basesExon 9: 36,759,727–36,759,841, 115 basesExon 8: 36,765,012–36,765,172, 161 basesExon 7: 36,767,218–36,767,285, 68 basesExon 6: 36,896,860–36,897,131, 272 basesExon 5: 36,930,251–36,930,433, 183 basesExon 4: 36,936,449–36,937,392, 944 basesExon 3: 36,938,832–36,938,994, 163 basesExon 2: 36,962,036–36,962,170, 135 basesExon 1: 36,966,444–36,966,669, 226 bases1110864215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 8.3 kb of the gene's 218 kb; 2,622 of those bases code for the protein.

How a genome test reads HLCS

204

positions in HLCS where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 218 kb of HLCS, introns included, not only the 8.3 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). HLCS gene: holocarboxylase synthetase. Retrieved 16 October 2026, from https://dantelabs.com/genes/hlcs

Vancouver

Dante Labs. HLCS gene: holocarboxylase synthetase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hlcs

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