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Gene

HMGCS2

3-hydroxy-3-methylglutaryl-CoA synthase 2

Summary

Cytogenetic location
1p12
Coordinates
Chromosome 1: 119,748,002–119,768,905 (GRCh38)
Exons
10 exons across 20.9 kb
Protein
508 amino acids
Inheritance
Autosomal recessive
MANE Select transcript
ENST00000369406.8NM_005518.4
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

  • Fatty Acid Oxidation & Carnitine Cycle Disorders

    • Disorders of Fatty Acid Oxidation and KetogenesisAutosomal recessive

      A group of enzyme and transporter defects, including MCAD, VLCAD, LCHAD, SCAD and HADH deficiency, primary carnitine deficiency and carnitine-acylcarnitine translocase deficiency, that can cause low blood sugar, muscle breakdown, heart and liver problems during periods of fasting or illness.

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

      Knowing allows avoidance of prolonged fasting, an emergency plan for illness and, where relevant, carnitine or dietary fat modification, which can prevent life-threatening episodes.

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 HMGCS2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where HMGCS2 sits. HMGCS2 and 9 genes near it on chromosome 1, from 119,258,454 to 120,258,453.Chromosome 11p12p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44119.4 Mb119.6 Mb119.8 Mb120 Mb120.2 MbHAO2: 119,368,727–119,394,258, forward strandHAO2HSD3B2: 119,413,725–119,453,802, forward strandHSD3B2HSD3B1: 119,493,057–119,529,426, forward strandHSD3B1ZNF697: 119,619,377–119,648,454, reverse strandZNF697PHGDH: 119,648,411–119,744,227, forward strandPHGDHHMGCS2: 119,748,002–119,768,905, reverse strandHMGCS2REG4: 119,794,017–119,811,580, reverse strandREG4ADAM30: 119,893,533–119,896,515, reverse strandADAM30NOTCH2: 119,909,256–120,100,779, reverse strandNOTCH2SEC22B: 120,150,898–120,176,533, reverse strandSEC22BDiagram of HMGCS2: 10 exons on the reverse strand of chromosome 1Exon 9: 3 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 7: 3 known disease-causing sitesExon 6: 4 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 4: 9 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 2: 9 known disease-causing sitesExon 1: 1 known disease-causing siteExon 10: 119,748,002–119,748,841, 840 basesExon 9: 119,750,797–119,750,908, 112 basesExon 8: 119,752,549–119,752,674, 126 basesExon 7: 119,753,280–119,753,386, 107 basesExon 6: 119,755,427–119,755,597, 171 basesExon 5: 119,757,273–119,757,438, 166 basesExon 4: 119,759,118–119,759,282, 165 basesExon 3: 119,759,864–119,759,989, 126 basesExon 2: 119,764,172–119,764,626, 455 basesExon 1: 119,768,741–119,768,905, 165 bases109876543215′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 2.4 kb of the gene's 20.9 kb; 1,527 of those bases code for the protein.

How a genome test reads HMGCS2

48

positions in HMGCS2 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 20.9 kb of HMGCS2, introns included, not only the 2.4 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.). HMGCS2 gene: 3-hydroxy-3-methylglutaryl-CoA synthase 2. Retrieved 16 October 2026, from https://dantelabs.com/genes/hmgcs2

Vancouver

Dante Labs. HMGCS2 gene: 3-hydroxy-3-methylglutaryl-CoA synthase 2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hmgcs2

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