HMGCS2

UniProt ID: P54868
Organism: Homo sapiens
Review Status: INITIALIZED
📝 Provide Detailed Feedback

Gene Description

HMGCS2 encodes the mitochondrial isoform of 3-hydroxy-3-methylglutaryl-CoA synthase (mitochondrial HMG-CoA synthase, mHS; EC 2.3.3.10), a homodimeric enzyme of the thiolase-like superfamily that catalyzes the first, committed and rate-limiting step of ketogenesis. Using an active-site cysteine (Cys166) to form an acyl-thioester intermediate, it condenses acetyl-CoA with acetoacetyl-CoA (and water) to yield (3S)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA), CoA and a proton; the HMG-CoA product is subsequently cleaved by mitochondrial HMG-CoA lyase (HMGCL) to acetoacetate, the first ketone body. The enzyme resides in the mitochondrial matrix and is expressed at very high levels in liver (roughly 200-fold above other tissues), with lower expression in colon, kidney, testis and pancreas. It is strongly induced during fasting/starvation, chiefly through PPAR-alpha/FGF21 signaling, and provides the ketone bodies that serve as an alternative fuel for the brain and peripheral tissues. Loss-of-function mutations cause mitochondrial HMG-CoA synthase deficiency (HMGCS2D; MIM 605911), an inborn error of metabolism presenting with fasting hypoketotic hypoglycemia, encephalopathy and hepatomegaly. HMGCS2 is distinct from the cytosolic paralog HMGCS1, which supplies HMG-CoA to the mevalonate/cholesterol biosynthetic pathway; unlike HMGCS1 and prokaryotic HMG-CoA synthases, mitochondrial HMGCS2 does not function in isoprenoid/sterol biosynthesis.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (IBA) assignment of the defining molecular function of HMGCS2, HMG-CoA synthase activity (EC 2.3.3.10). This is the enzyme's core, experimentally established catalytic activity and the term is at the correct level of specificity.
Reason: HMG-CoA synthase activity is the primary molecular function of HMGCS2 and is independently supported by direct experimental evidence in human (EXP/IMP). The IBA call is consistent across the orthologous panel including the human, mouse and rat mitochondrial enzymes.
Supporting Evidence:
PMID:29597274
catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
GO:0006084 acetyl-CoA metabolic process
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (IBA) involvement in acetyl-CoA metabolism. Acetyl-CoA is a direct substrate of the HMG-CoA synthase reaction, so this broad metabolic-process term is biologically correct, though generic relative to the enzyme's specific role in ketone body biosynthesis.
Reason: The enzyme consumes acetyl-CoA (and acetoacetyl-CoA) in its condensation reaction, so involvement in acetyl-CoA metabolic process is accurate. It is a broad parent term and is non-core relative to ketone body biosynthetic process, but not incorrect.
Supporting Evidence:
PMID:29597274
catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
GO:0005739 mitochondrion
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (IBA) assignment of mitochondrial localization/activity. HMGCS2 carries an N-terminal mitochondrial transit peptide (residues 1-37) and functions in the mitochondrial matrix; this is consistent with the mitochondrial isoform.
Reason: Correct compartment for the mitochondrial isoform. The more precise term (mitochondrial matrix, GO:0005759) is also annotated; mitochondrion is an accurate parent and the is_active_in qualifier is appropriate for an active matrix enzyme.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Electronic (UniProt/ARBA + RHEA/EC:2.3.3.10) assignment of HMG-CoA synthase activity. Redundant with the experimental, IBA and ISS calls for the same term and at the correct specificity.
Reason: Matches the experimentally established catalytic activity (RHEA:10188, EC 2.3.3.10). Duplication across evidence codes is acceptable.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
EC=2.3.3.10
GO:0005739 mitochondrion
IEA
GO_REF:0000120 		ACCEPT
Summary: Electronic assignment of mitochondrial localization (UniProt SubCell SL-0173, ortholog transfer). Correct compartment for the mitochondrial isoform.
Reason: Consistent with the transit peptide and matrix localization; redundant with other mitochondrion/matrix annotations.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0006084 acetyl-CoA metabolic process
IEA
GO_REF:0000002 		ACCEPT
Summary: InterPro2GO electronic assignment of acetyl-CoA metabolic process. Biologically correct (acetyl-CoA is a substrate), though broad; redundant with the IBA/IMP calls for the same term.
Reason: Accurate broad metabolic-process term; acetyl-CoA is consumed by the reaction.
Supporting Evidence:
PMID:29597274
catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
GO:0008299 isoprenoid biosynthetic process
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: InterPro2GO electronic assignment of isoprenoid biosynthetic process, transferred from the pan-HMGCS InterPro families (IPR000590, IPR010122). This role belongs to the cytosolic/prokaryotic HMG-CoA synthases that feed the mevalonate/isoprenoid pathway, NOT to the mitochondrial ketogenic isoform HMGCS2.
Reason: HMGCS2 is the mitochondrial isoform whose product HMG-CoA is committed to ketogenesis (cleaved by HMGCL to acetoacetate), not to mevalonate/isoprenoid synthesis. The isoprenoid role is a paralog function of HMGCS1 (cytosolic) and of prokaryotic HMGCS; the InterPro family term is over-propagated across all HMG-CoA synthases. PMID:20346956 explicitly separates the mitochondrial isoform (ketone body formation) from the cytosolic isoform (mevalonate pathway, end product cholesterol).
Supporting Evidence:
PMID:20346956
Mammals also contain a mitochondrial isoform; its
PMID:7851882
whereas the cytoplasmic HS isozyme (cHS) mediates an early step
GO:0016746 acyltransferase activity
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro electronic assignment of the broad acyltransferase-activity term based on the thiolase-like fold (IPR016039). This is a distant parent of the specific and experimentally established HMG-CoA synthase activity.
Reason: Too general. The enzyme's actual acyl-transfer chemistry is captured precisely by GO:0004421 (hydroxymethylglutaryl-CoA synthase activity), which is already annotated with experimental support. Replace with the specific term.
Supporting Evidence:
PMID:29597274
catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
GO:0001822 kidney development
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer from the rat ortholog (RGD phenotype/expression annotation) of kidney development. HMGCS2 is expressed at low levels in kidney but there is no evidence its catalytic activity drives kidney organogenesis.
Reason: Automatic phenotype/expression transfer that conflates tissue expression with a developmental role. HMGCS2 is a ketogenic metabolic enzyme; a specific function in kidney development is not supported and this term over-annotates the gene.
GO:0001889 liver development
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of liver development from the rat ortholog. HMGCS2 is very highly expressed in liver, but its role there is ketogenesis, not driving liver organogenesis.
Reason: Reflects high hepatic expression rather than a demonstrated developmental function. Over-annotation for a metabolic enzyme.
GO:0005759 mitochondrial matrix
IEA
GO_REF:0000107 		ACCEPT
Summary: Ensembl-Compara electronic transfer of mitochondrial matrix localization from the rat ortholog. This is the precise, correct subcellular compartment for HMGCS2.
Reason: Matrix localization is correct for this matrix-soluble ketogenic enzyme and is corroborated by Reactome TAS annotations to the same term.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0007494 midgut development
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of midgut development from the rat ortholog. Not supported by any evidence of a developmental role for HMGCS2.
Reason: Automatic ortholog transfer that over-annotates a metabolic enzyme with an unrelated developmental process.
GO:0007584 response to nutrient
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to nutrient. HMGCS2 expression and activity are indeed nutritionally regulated (fasting induction), so a nutrient-response annotation is biologically plausible, though it captures regulation of the gene rather than a distinct process the protein carries out.
Reason: Consistent with the well-documented nutritional/fasting regulation of ketogenesis, but peripheral to the enzyme's core catalytic function.
GO:0009266 response to temperature stimulus
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to temperature stimulus from the rat ortholog. No specific evidence links HMGCS2 catalytic function to temperature responses.
Reason: Non-specific ortholog phenotype transfer; over-annotation for this enzyme.
GO:0009410 response to xenobiotic stimulus
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to xenobiotic stimulus. Not substantiated for HMGCS2's molecular function.
Reason: Automatic ortholog transfer without evidence of a direct role; over-annotation.
GO:0009617 response to bacterium
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to bacterium. Not supported for HMGCS2.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0010038 response to metal ion
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to metal ion. Not supported for HMGCS2.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0030324 lung development
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of lung development from the rat ortholog. No evidence of a developmental role for HMGCS2 in lung.
Reason: Automatic ortholog transfer that over-annotates a metabolic enzyme with an unrelated developmental process.
GO:0032868 response to insulin
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to insulin. HMGCS2 transcription is reciprocally regulated by insulin/glucagon (suppressed in the fed state), so a response-to-insulin annotation reflects known regulation of the gene rather than a distinct molecular activity.
Reason: Plausible given hormonal (insulin) regulation of ketogenic gene expression; peripheral to the enzyme's catalytic function.
GO:0032869 cellular response to insulin stimulus
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of cellular response to insulin stimulus. As with response to insulin, reflects hormonal regulation of the gene.
Reason: Consistent with insulin regulation of ketogenic gene expression; non-core.
GO:0032870 cellular response to hormone stimulus
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of cellular response to hormone stimulus. HMGCS2 is regulated by several hormones (glucagon, insulin, glucocorticoids), so this broad term captures regulation of expression rather than the protein's own function.
Reason: Broad hormone-response term consistent with documented hormonal regulation of the ketogenic program; peripheral to catalytic function.
GO:0033555 multicellular organismal response to stress
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of a very broad organism-level stress-response term. Not informative for the enzyme's molecular role.
Reason: Overly general organism-level term from automatic ortholog transfer; over-annotation.
GO:0033574 response to testosterone
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to testosterone. Not substantiated for HMGCS2.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0033762 response to glucagon
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to glucagon. Glucagon (via cAMP) is a principal inducer of hepatic ketogenesis and HMGCS2 transcription during fasting, so this annotation reflects a well-established regulatory input.
Reason: Consistent with glucagon/cAMP induction of ketogenic gene expression during fasting; peripheral to the enzyme's catalytic function but biologically grounded.
GO:0034014 response to triglyceride
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to triglyceride. Not specifically supported for HMGCS2's function.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0034284 response to monosaccharide
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to monosaccharide (e.g., glucose). Glucose availability reciprocally regulates ketogenesis, so this is a plausible regulatory annotation but peripheral to function.
Reason: Consistent with glucose/carbohydrate regulation of ketogenic gene expression; non-core.
GO:0034696 response to prostaglandin F
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to prostaglandin F. Not substantiated for HMGCS2.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0042594 response to starvation
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to starvation. Fasting/starvation is the central physiological trigger for HMGCS2-driven ketogenesis and induces HMGCS2 expression, so this is among the most biologically relevant of the response-to-X terms.
Reason: Well-grounded in the fasting physiology of ketogenesis (HMGCS2 is induced during starvation), but describes the physiological context rather than the enzyme's molecular activity, so it is retained as non-core.
GO:0043434 response to peptide hormone
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to peptide hormone (broad parent of the insulin/glucagon responses). Reflects hormonal regulation of ketogenic gene expression.
Reason: Broad hormone-response term consistent with documented hormonal regulation; non-core.
GO:0045471 response to ethanol
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to ethanol. Not specifically supported for HMGCS2's molecular function.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0046951 ketone body biosynthetic process
IEA
GO_REF:0000107 		ACCEPT
Summary: Ensembl-Compara electronic transfer of ketone body biosynthetic process. This is the core biological process of HMGCS2 and is independently supported by human IMP and Reactome TAS evidence.
Reason: Ketone body biosynthesis is the defining physiological role of HMGCS2 (the rate-limiting step of ketogenesis). Correct and well-supported; redundant with the IMP/TAS calls.
Supporting Evidence:
PMID:23751782
that affects ketone-body synthesis.
GO:0051384 response to glucocorticoid
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to glucocorticoid. Glucocorticoids contribute to induction of the fasting/ketogenic program, so this is a plausible regulatory annotation.
Reason: Consistent with hormonal (glucocorticoid) regulation of ketogenic gene expression; peripheral to catalytic function.
GO:0051591 response to cAMP
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to cAMP. cAMP is the second messenger of glucagon signaling that induces hepatic ketogenesis and HMGCS2 expression, so this term reflects a genuine regulatory pathway.
Reason: Consistent with cAMP/glucagon induction of the ketogenic program; non-core relative to the enzyme's activity.
GO:0060416 response to growth hormone
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to growth hormone. Not specifically substantiated for HMGCS2.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0060612 adipose tissue development
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of adipose tissue development from the rat ortholog. No evidence of a developmental role for HMGCS2 in adipose tissue.
Reason: Automatic ortholog transfer that over-annotates a metabolic enzyme with an unrelated developmental process.
GO:0070542 response to fatty acid
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of response to fatty acid. Fatty acids (via PPAR-alpha) induce the ketogenic program including HMGCS2, so this is a biologically grounded regulatory annotation.
Reason: Consistent with fatty-acid/PPAR-alpha induction of HMGCS2 during fasting; peripheral to the catalytic function.
GO:0070543 response to linoleic acid
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of response to a specific fatty acid (linoleic acid). More specific than can be justified for HMGCS2 beyond the general fatty-acid response.
Reason: Overly specific ortholog transfer; the general response to fatty acid already captures the relevant regulatory input.
GO:0071222 cellular response to lipopolysaccharide
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of cellular response to lipopolysaccharide. Not specifically supported for HMGCS2's function.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0071230 cellular response to amino acid stimulus
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: Ensembl-Compara electronic transfer of cellular response to amino acid stimulus. Not specifically substantiated for HMGCS2.
Reason: Non-specific ortholog phenotype transfer; over-annotation.
GO:0071385 cellular response to glucocorticoid stimulus
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of cellular response to glucocorticoid stimulus. Reflects glucocorticoid regulation of the ketogenic program.
Reason: Consistent with hormonal (glucocorticoid) regulation of HMGCS2 expression; non-core.
GO:0071398 cellular response to fatty acid
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl-Compara electronic transfer of cellular response to fatty acid. Reflects fatty-acid/PPAR-alpha induction of the ketogenic program.
Reason: Consistent with fatty-acid regulation of HMGCS2; peripheral to catalytic function.
GO:0046951 ketone body biosynthetic process
TAS
Reactome:R-HSA-77111 		ACCEPT
Summary: Reactome traceable-author-statement placing HMGCS2 in the Synthesis of Ketone Bodies pathway. This is the core biological process of the enzyme.
Reason: Reactome curates HMGCS2 as the enzyme catalyzing the committed step of ketone body synthesis, consistent with all experimental and phylogenetic evidence.
Supporting Evidence:
PMID:23751782
that affects ketone-body synthesis.
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
TAS
Reactome:R-HSA-73918 		ACCEPT
Summary: Reactome TAS for the HMG-CoA synthase reaction (acetoacetyl-CoA + acetyl-CoA => HMG-CoA + CoASH). Core molecular function.
Reason: Directly describes the enzyme's catalyzed reaction; consistent with experimental evidence and the correct level of specificity.
Supporting Evidence:
PMID:20346956
condensation of acetyl-CoA and acetoacetyl-CoA into 3-hydroxy-3-methylglutaryl
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
EXP
PMID:11228257
Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase defici... 		ACCEPT
Summary: Direct experimental (EXP) evidence for HMG-CoA synthase activity. This study characterized wild-type and the F174L disease variant of human mHS by bacterial expression and activity assay, establishing the catalytic function.
Reason: Experimental characterization of the human enzyme's HMG-CoA synthase activity, with the F174L patient variant abolishing detectable activity. This is a definitive, core MF annotation.
Supporting Evidence:
PMID:11228257
F174L-mHS produces a low level of mHS polypeptide with no detectable activity.
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
EXP
PMID:29597274
Human Mitochondrial HMG-CoA Synthase Deficiency: Role of Enz... 		ACCEPT
Summary: Direct experimental (EXP) evidence for HMG-CoA synthase activity. This study expressed wild-type human mHS and measured its activity relative to numerous disease variants, confirming the condensation reaction of ketone body synthesis.
Reason: Experimental measurement of human mHS enzymatic activity; core MF annotation supported by quantitative enzyme assays.
Supporting Evidence:
PMID:29597274
catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
GO:0005739 mitochondrion
ISS
GO_REF:0000024 		ACCEPT
Summary: ISS (sequence-similarity) assignment of mitochondrial localization, transferred from the rat ortholog P22791. Correct compartment for the mitochondrial isoform bearing an N-terminal transit peptide.
Reason: Consistent with the mitochondrial transit peptide and matrix localization; redundant with the mitochondrion/matrix annotations from other sources.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0005739 mitochondrion
HTP
PMID:34800366
Quantitative high-confidence human mitochondrial proteome an... 		ACCEPT
Summary: High-throughput mass-spectrometry evidence (MitoCoP high-confidence human mitochondrial proteome) placing HMGCS2 in mitochondria. Consistent with its established matrix localization.
Reason: Large-scale proteomic detection in the high-confidence mitochondrial proteome supports mitochondrial localization, corroborating the manual/ISS/IBA annotations.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0042802 identical protein binding
IDA
PMID:20346956
Crystal structures of human HMG-CoA synthase isoforms provid... 		KEEP AS NON CORE
Summary: IDA annotation of identical protein binding based on the crystal structure of human HMGCS2 (PDB 2WYA), which shows the enzyme is a homodimer. The homodimeric assembly is a real structural property, but "identical protein binding" is an uninformative molecular function term relative to the enzyme's catalytic role.
Reason: The homodimer is structurally established (self-association is genuine), so per curation policy this experimental self-binding annotation is retained rather than removed, but it is uninformative about the enzyme's function and is therefore marked non-core.
Supporting Evidence:
PMID:29597274
Previous studies have already pointed out that mHS is a homodimeric enzyme
PMID:29597274
which was subsequently confirmed by the crystallization of the enzyme
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
IMP
PMID:23751782
New case of mitochondrial HMG-CoA synthase deficiency. Funct... 		ACCEPT
Summary: IMP evidence for HMG-CoA synthase activity: the study developed a method to express human mHS and measured the effect of eight disease mutations on catalytic activity, demonstrating the enzyme's function through loss-of-activity variants.
Reason: Functional analysis of patient mutations (total loss or reduced catalytic efficiency) directly demonstrates HMGCS2's HMG-CoA synthase activity. Core MF annotation.
Supporting Evidence:
PMID:23751782
an enzyme with a catalytic efficiency of 11.5%.
GO:0006084 acetyl-CoA metabolic process
IMP
PMID:23751782
New case of mitochondrial HMG-CoA synthase deficiency. Funct... 		ACCEPT
Summary: IMP involvement in acetyl-CoA metabolic process, inferred from mutation analysis of the HMG-CoA synthase reaction (which consumes acetyl-CoA). Correct but broad.
Reason: Acetyl-CoA is a direct substrate of the reaction assayed in this mutation study; the broad metabolic-process term is accurate though non-core relative to ketogenesis.
Supporting Evidence:
PMID:29597274
catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
GO:0046951 ketone body biosynthetic process
IMP
PMID:23751782
New case of mitochondrial HMG-CoA synthase deficiency. Funct... 		ACCEPT
Summary: IMP involvement in ketone body biosynthetic process, based on functional analysis of disease mutations that impair ketogenesis. This is the core biological process of HMGCS2.
Reason: The study links HMGCS2 mutations to a disorder that affects ketone-body synthesis and characterizes the associated loss of enzyme activity, directly supporting the ketogenesis annotation. Core BP annotation.
Supporting Evidence:
PMID:23751782
that affects ketone-body synthesis.
GO:0004421 hydroxymethylglutaryl-CoA synthase activity
ISS
GO_REF:0000024 		ACCEPT
Summary: ISS assignment of HMG-CoA synthase activity, transferred from the human cytosolic paralog HMGCS1 (P54869). Redundant with the experimental evidence for the same term at the correct specificity.
Reason: The catalytic activity is correct and experimentally established for HMGCS2; the ISS transfer converges on the right molecular function despite being based on the paralog.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
EC=2.3.3.10
GO:0005759 mitochondrial matrix
TAS
Reactome:R-HSA-1989760 		ACCEPT
Summary: Reactome TAS for mitochondrial matrix localization (Expression of HMGCS2 pathway). This is the precise, correct compartment for the enzyme.
Reason: Matrix localization is correct for this matrix-soluble ketogenic enzyme; consistent with the transit peptide and other matrix/mitochondrion annotations.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0005759 mitochondrial matrix
TAS
Reactome:R-HSA-73918 		ACCEPT
Summary: Reactome TAS for mitochondrial matrix localization, associated with the HMG-CoA synthase reaction. Correct compartment.
Reason: Matrix localization corroborated across multiple Reactome events and the transit peptide.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0005759 mitochondrial matrix
TAS
Reactome:R-HSA-9838081 		ACCEPT
Summary: Reactome TAS for mitochondrial matrix localization, in the context of LONP1-mediated degradation of matrix proteins. Correct compartment; annotation reflects HMGCS2 being a matrix substrate of the LONP1 quality-control machinery.
Reason: The matrix localization is correct. The associated pathway (LONP1 degrades matrix proteins) concerns turnover of HMGCS2 rather than its ketogenic function, but the cellular-component call is accurate.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0005759 mitochondrial matrix
TAS
Reactome:R-HSA-9838093 		ACCEPT
Summary: Reactome TAS for mitochondrial matrix localization, in the context of LONP1 binding matrix proteins. Correct compartment.
Reason: Matrix localization is accurate; the pathway concerns HMGCS2 as a LONP1 client, not its catalytic role, but the compartment annotation is correct.
Supporting Evidence:
file:human/HMGCS2/HMGCS2-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion
GO:0005739 mitochondrion
TAS
PMID:7851882
Human mitochondrial HMG CoA synthase: liver cDNA and partial... 		ACCEPT
Summary: TAS (from the original human liver mHS cloning paper) for mitochondrial localization. The paper established mHS as the first enzyme of ketogenesis, distinct from the cytosolic cholesterol-synthesis isozyme, and mitochondrial localization is intrinsic to that distinction.
Reason: Foundational reference identifying the mitochondrial HMG-CoA synthase; the mitochondrion annotation is correct and consistent with all downstream evidence.
Supporting Evidence:
PMID:7851882
whereas the cytoplasmic HS isozyme (cHS) mediates an early step

Core Functions

Catalyzes the committed, rate-limiting step of ketogenesis in the mitochondrial matrix: the condensation of acetyl-CoA with acetoacetyl-CoA to form (3S)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) plus CoA, via an active-site cysteine acyl-thioester intermediate.

Molecular Function:
hydroxymethylglutaryl-CoA synthase activity
Directly Involved In:
ketone body biosynthetic process
Cellular Locations:
mitochondrial matrix
Supporting Evidence:
  • PMID:29597274
    catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
  • file:human/HMGCS2/HMGCS2-uniprot.txt
    Catalyzes the first irreversible step in ketogenesis,

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000024
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
GO_REF:0000033
Annotation inferences using phylogenetic trees
GO_REF:0000107
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
GO_REF:0000120
Combined Automated Annotation using Multiple IEA Methods
PMID:11228257
Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency: clinical course and description of causal mutations in two patients.
PMID:20346956
Crystal structures of human HMG-CoA synthase isoforms provide insights into inherited ketogenesis disorders and inhibitor design.
PMID:23751782
New case of mitochondrial HMG-CoA synthase deficiency. Functional analysis of eight mutations.
PMID:29597274
Human Mitochondrial HMG-CoA Synthase Deficiency: Role of Enzyme Dimerization Surface and Characterization of Three New Patients.
PMID:34800366
Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
PMID:7851882
Human mitochondrial HMG CoA synthase: liver cDNA and partial genomic cloning, chromosome mapping to 1p12-p13, and possible role in vertebrate evolution.
Reactome:R-HSA-1989760
Expression of HMGCS2
Reactome:R-HSA-73918
acetoacetyl-CoA+acetyl-CoA => HMG-CoA + CoASH
Reactome:R-HSA-77111
Synthesis of Ketone Bodies
Reactome:R-HSA-9838081
LONP1 degrades mitochondrial matrix proteins
Reactome:R-HSA-9838093
LONP1 binds mitochondrial matrix proteins

Suggested Questions for Experts

Q: Do the acetylation/succinylation PTMs of HMGCS2 (e.g., at Lys-83/Lys-310) and their reversal by SIRT3/SIRT5 provide physiologically significant control of ketogenic flux in human liver, beyond transcriptional (PPAR-alpha/FGF21) regulation?

Q: What, if any, is the function of the muscle/heart-enriched isoform 3 (HMGCS2delta4), and does it retain HMG-CoA synthase activity?

Suggested Experiments

Experiment: Quantify ketogenic flux (labeled acetyl-CoA to beta-hydroxybutyrate) in primary human hepatocytes with HMGCS2 knockdown/knockout versus rescue with wild-type and PTM-site mutants to test the contribution of acetylation/succinylation to activity control.

Experiment: Express and assay HMGCS2 isoform 3 (HMGCS2delta4) in parallel with isoform 1 to determine whether the muscle/heart-enriched splice variant retains catalytic activity or has a distinct role.

📚 Additional Documentation

Notes

(HMGCS2-notes.md)

HMGCS2 (P54868) review notes

Deep research status

  • just deep-research-falcon human HMGCS2 FAILED in this worktree: scripts/deep_research_wrapper.py
    raises TypeError: unsupported operand type(s) for |: 'type' and 'NoneType' at line 158
    (uniprot_context: dict | None = None) — the wrapper uses PEP 604 union syntax under a Python
    interpreter that does not support it. This is a tooling/env issue, not a transient failure, so no
    HMGCS2-deep-research-falcon.md was produced. Did NOT fabricate a deep-research file.
  • Review grounded instead in: HMGCS2-uniprot.txt (P54868), seeded GOA (HMGCS2-goa.tsv),
    the disorder KB ~/repos/dismech/kb/disorders/3-Hydroxy-3-Methylglutaryl-CoA_Synthase_Deficiency.yaml,
    and cached publications/PMID_*.md.

Verified core biology

  • HMGCS2 = mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase (mHS), EC 2.3.3.10.
  • Catalytic activity (UniProt CATALYTIC ACTIVITY / RHEA:10188):
    acetoacetyl-CoA + acetyl-CoA + H2O = (3S)-3-hydroxy-3-methylglutaryl-CoA + CoA + H(+).
  • It is the FIRST, rate-limiting/committed step of ketogenesis (ketone body biosynthesis), chiefly in
    liver during fasting; HMG-CoA product is then cleaved by HMG-CoA lyase (HMGCL) to acetoacetate.
    [file:HMGCS2-uniprot.txt "Catalyzes the first irreversible step in ketogenesis"]
    Disorder KB: "which is the rate-limiting step of ketone body synthesis"; "the rate-limiting step of ketogenesis".
  • Localization: mitochondrion / mitochondrial matrix. UniProt SUBCELLULAR LOCATION: Mitochondrion (ISS
    from rat P22791). Reactome and Ensembl place it in mitochondrial matrix.
  • Homodimer (crystal structure PMID:20346956, PDB 2WYA); catalytic Cys166 (acyl-thioester intermediate).
  • Tissue: liver expression ~200-fold higher than any other tissue; induced during fasting.
  • Distinct from CYTOSOLIC HMGCS1 (P54868 is mitochondrial; HMGCS1/P54869 is cytosolic mevalonate/
    cholesterol pathway). PMID:20346956 and PMID:7851882 make the mHS vs cHS distinction explicit.
  • Disease: mitochondrial HMG-CoA synthase deficiency (HMGCS2D, MIM 605911): fasting hypoketotic
    hypoglycemia, encephalopathy, hepatomegaly.

Annotation-level notes

  • MF GO:0004421 (HMG-CoA synthase activity): strongly supported — EXP (PMID:11228257, PMID:29597274),
    IMP (PMID:23751782), IBA, ISS, TAS Reactome, IEA. CORE. All ACCEPT (dedup fine per guidelines).
  • BP GO:0046951 (ketone body biosynthetic process): CORE — IMP (PMID:23751782), TAS Reactome, IEA. ACCEPT.
  • BP GO:0006084 (acetyl-CoA metabolic process): correct but broad parent of the reaction; the enzyme
    consumes acetyl-CoA. Keep (ACCEPT the IMP/IBA; the acetyl-CoA is a substrate). Non-core relative to
    ketogenesis but not wrong.
  • CC GO:0005739 mitochondrion / GO:0005759 mitochondrial matrix: correct; matrix is the more precise term.
  • GO:0008299 isoprenoid biosynthetic process (InterPro2GO IEA): This is the CYTOSOLIC/prokaryotic
    HMGCS role (mevalonate/isoprenoid). HMGCS2 is the mitochondrial ketogenic isoform; it does NOT
    function in isoprenoid biosynthesis in vivo. InterPro family term over-propagated across all HMGCS.
    UniProt PATHWAY line "(R)-mevalonate biosynthesis ... step 2/3" and KW "Cholesterol biosynthesis" are
    family-level/paralog-derived and biologically incorrect for the mitochondrial ketogenic enzyme.
    MARK_AS_OVER_ANNOTATED (wrong-branch family transfer; the mitochondrial isoform does not make isoprenoids).
  • GO:0016746 acyltransferase activity (InterPro IEA, thiolase-like fold): correct but far too general
    parent of GO:0004421. MODIFY -> GO:0004421.
  • GO:0042802 identical protein binding (IDA, PMID:20346956): supported by crystal-structure homodimer.
    Per policy, do not REMOVE bare protein-binding IPI/IDA; keep as non-core (homodimer is structurally
    real but "identical protein binding" is uninformative vs the enzyme's function). KEEP_AS_NON_CORE.
  • Large Ensembl-Compara "response to X" / "development" IEA block (GO_REF:0000107): transferred from rat
    ortholog RGD phenotype/expression annotations. HMGCS2 is transcriptionally regulated by fasting/PPARa/
    glucagon/cAMP/insulin etc., so many "response to hormone/nutrient" terms reflect regulation-of-expression
    rather than the gene product's own molecular activity in that process. These are peripheral. Keep the
    well-supported physiological ones as non-core; the many overly specific / developmental ones are
    over-annotations. Given they are IEA phenotype transfers (not experimental for HMGCS2), and per policy
    IEA over-propagation may be argued against, mark the clearly peripheral/organ-development ones
    MARK_AS_OVER_ANNOTATED and keep response-to-fasting/starvation/glucagon-type as non-core where they
    reflect known regulation.

📄 View Raw YAML

 
id: P54868
gene_symbol: HMGCS2
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  HMGCS2 encodes the mitochondrial isoform of 3-hydroxy-3-methylglutaryl-CoA synthase
  (mitochondrial HMG-CoA synthase, mHS; EC 2.3.3.10), a homodimeric enzyme of the
  thiolase-like superfamily that catalyzes the first, committed and rate-limiting step of
  ketogenesis. Using an active-site cysteine (Cys166) to form an acyl-thioester
  intermediate, it condenses acetyl-CoA with acetoacetyl-CoA (and water) to yield
  (3S)-3-hydroxy-3-methylglutaryl-CoA (HMG-CoA), CoA and a proton; the HMG-CoA product is
  subsequently cleaved by mitochondrial HMG-CoA lyase (HMGCL) to acetoacetate, the first
  ketone body. The enzyme resides in the mitochondrial matrix and is expressed at very high
  levels in liver (roughly 200-fold above other tissues), with lower expression in colon,
  kidney, testis and pancreas. It is strongly induced during fasting/starvation, chiefly
  through PPAR-alpha/FGF21 signaling, and provides the ketone bodies that serve as an
  alternative fuel for the brain and peripheral tissues. Loss-of-function mutations cause
  mitochondrial HMG-CoA synthase deficiency (HMGCS2D; MIM 605911), an inborn error of
  metabolism presenting with fasting hypoketotic hypoglycemia, encephalopathy and
  hepatomegaly. HMGCS2 is distinct from the cytosolic paralog HMGCS1, which supplies HMG-CoA
  to the mevalonate/cholesterol biosynthetic pathway; unlike HMGCS1 and prokaryotic HMG-CoA
  synthases, mitochondrial HMGCS2 does not function in isoprenoid/sterol biosynthesis.
alternative_products:
- name: '1'
  id: P54868-1
- name: '2'
  id: P54868-2
  sequence_note: VSP_042892
- name: 3 (HMGCS2delta4 {ECO:0000303|PubMed:21952825})
  id: P54868-3
  sequence_note: VSP_047445
existing_annotations:
- term:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic (IBA) assignment of the defining molecular function of HMGCS2, HMG-CoA
      synthase activity (EC 2.3.3.10). This is the enzyme's core, experimentally established
      catalytic activity and the term is at the correct level of specificity.
    action: ACCEPT
    reason: >-
      HMG-CoA synthase activity is the primary molecular function of HMGCS2 and is
      independently supported by direct experimental evidence in human (EXP/IMP). The IBA
      call is consistent across the orthologous panel including the human, mouse and rat
      mitochondrial enzymes.
    supported_by:
    - reference_id: PMID:29597274
      supporting_text: catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
- term:
    id: GO:0006084
    label: acetyl-CoA metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic (IBA) involvement in acetyl-CoA metabolism. Acetyl-CoA is a direct
      substrate of the HMG-CoA synthase reaction, so this broad metabolic-process term is
      biologically correct, though generic relative to the enzyme's specific role in
      ketone body biosynthesis.
    action: ACCEPT
    reason: >-
      The enzyme consumes acetyl-CoA (and acetoacetyl-CoA) in its condensation reaction, so
      involvement in acetyl-CoA metabolic process is accurate. It is a broad parent term and
      is non-core relative to ketone body biosynthetic process, but not incorrect.
    supported_by:
    - reference_id: PMID:29597274
      supporting_text: catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      Phylogenetic (IBA) assignment of mitochondrial localization/activity. HMGCS2 carries an
      N-terminal mitochondrial transit peptide (residues 1-37) and functions in the
      mitochondrial matrix; this is consistent with the mitochondrial isoform.
    action: ACCEPT
    reason: >-
      Correct compartment for the mitochondrial isoform. The more precise term
      (mitochondrial matrix, GO:0005759) is also annotated; mitochondrion is an accurate
      parent and the is_active_in qualifier is appropriate for an active matrix enzyme.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic (UniProt/ARBA + RHEA/EC:2.3.3.10) assignment of HMG-CoA synthase activity.
      Redundant with the experimental, IBA and ISS calls for the same term and at the
      correct specificity.
    action: ACCEPT
    reason: >-
      Matches the experimentally established catalytic activity (RHEA:10188, EC 2.3.3.10).
      Duplication across evidence codes is acceptable.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: EC=2.3.3.10
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      Electronic assignment of mitochondrial localization (UniProt SubCell SL-0173, ortholog
      transfer). Correct compartment for the mitochondrial isoform.
    action: ACCEPT
    reason: >-
      Consistent with the transit peptide and matrix localization; redundant with other
      mitochondrion/matrix annotations.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0006084
    label: acetyl-CoA metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro2GO electronic assignment of acetyl-CoA metabolic process. Biologically correct
      (acetyl-CoA is a substrate), though broad; redundant with the IBA/IMP calls for the
      same term.
    action: ACCEPT
    reason: >-
      Accurate broad metabolic-process term; acetyl-CoA is consumed by the reaction.
    supported_by:
    - reference_id: PMID:29597274
      supporting_text: catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
- term:
    id: GO:0008299
    label: isoprenoid biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro2GO electronic assignment of isoprenoid biosynthetic process, transferred from
      the pan-HMGCS InterPro families (IPR000590, IPR010122). This role belongs to the
      cytosolic/prokaryotic HMG-CoA synthases that feed the mevalonate/isoprenoid pathway,
      NOT to the mitochondrial ketogenic isoform HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      HMGCS2 is the mitochondrial isoform whose product HMG-CoA is committed to ketogenesis
      (cleaved by HMGCL to acetoacetate), not to mevalonate/isoprenoid synthesis. The
      isoprenoid role is a paralog function of HMGCS1 (cytosolic) and of prokaryotic HMGCS;
      the InterPro family term is over-propagated across all HMG-CoA synthases. PMID:20346956
      explicitly separates the mitochondrial isoform (ketone body formation) from the
      cytosolic isoform (mevalonate pathway, end product cholesterol).
    supported_by:
    - reference_id: PMID:20346956
      supporting_text: 'Mammals also contain a mitochondrial isoform; its'
    - reference_id: PMID:7851882
      supporting_text: whereas the cytoplasmic HS isozyme (cHS) mediates an early step
- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro electronic assignment of the broad acyltransferase-activity term based on the
      thiolase-like fold (IPR016039). This is a distant parent of the specific and
      experimentally established HMG-CoA synthase activity.
    action: MODIFY
    reason: >-
      Too general. The enzyme's actual acyl-transfer chemistry is captured precisely by
      GO:0004421 (hydroxymethylglutaryl-CoA synthase activity), which is already annotated
      with experimental support. Replace with the specific term.
    proposed_replacement_terms:
    - id: GO:0004421
      label: hydroxymethylglutaryl-CoA synthase activity
    supported_by:
    - reference_id: PMID:29597274
      supporting_text: catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
- term:
    id: GO:0001822
    label: kidney development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer from the rat ortholog (RGD phenotype/expression
      annotation) of kidney development. HMGCS2 is expressed at low levels in kidney but
      there is no evidence its catalytic activity drives kidney organogenesis.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Automatic phenotype/expression transfer that conflates tissue expression with a
      developmental role. HMGCS2 is a ketogenic metabolic enzyme; a specific function in
      kidney development is not supported and this term over-annotates the gene.
- term:
    id: GO:0001889
    label: liver development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of liver development from the rat ortholog. HMGCS2
      is very highly expressed in liver, but its role there is ketogenesis, not driving liver
      organogenesis.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Reflects high hepatic expression rather than a demonstrated developmental function.
      Over-annotation for a metabolic enzyme.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of mitochondrial matrix localization from the rat
      ortholog. This is the precise, correct subcellular compartment for HMGCS2.
    action: ACCEPT
    reason: >-
      Matrix localization is correct for this matrix-soluble ketogenic enzyme and is
      corroborated by Reactome TAS annotations to the same term.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0007494
    label: midgut development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of midgut development from the rat ortholog. Not
      supported by any evidence of a developmental role for HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Automatic ortholog transfer that over-annotates a metabolic enzyme with an unrelated
      developmental process.
- term:
    id: GO:0007584
    label: response to nutrient
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to nutrient. HMGCS2 expression and
      activity are indeed nutritionally regulated (fasting induction), so a nutrient-response
      annotation is biologically plausible, though it captures regulation of the gene rather
      than a distinct process the protein carries out.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with the well-documented nutritional/fasting regulation of ketogenesis, but
      peripheral to the enzyme's core catalytic function.
- term:
    id: GO:0009266
    label: response to temperature stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to temperature stimulus from the rat
      ortholog. No specific evidence links HMGCS2 catalytic function to temperature responses.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation for this enzyme.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to xenobiotic stimulus. Not
      substantiated for HMGCS2's molecular function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Automatic ortholog transfer without evidence of a direct role; over-annotation.
- term:
    id: GO:0009617
    label: response to bacterium
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to bacterium. Not supported for HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0010038
    label: response to metal ion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to metal ion. Not supported for HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0030324
    label: lung development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of lung development from the rat ortholog. No
      evidence of a developmental role for HMGCS2 in lung.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Automatic ortholog transfer that over-annotates a metabolic enzyme with an unrelated
      developmental process.
- term:
    id: GO:0032868
    label: response to insulin
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to insulin. HMGCS2 transcription is
      reciprocally regulated by insulin/glucagon (suppressed in the fed state), so a
      response-to-insulin annotation reflects known regulation of the gene rather than a
      distinct molecular activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Plausible given hormonal (insulin) regulation of ketogenic gene expression; peripheral
      to the enzyme's catalytic function.
- term:
    id: GO:0032869
    label: cellular response to insulin stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of cellular response to insulin stimulus. As with
      response to insulin, reflects hormonal regulation of the gene.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with insulin regulation of ketogenic gene expression; non-core.
- term:
    id: GO:0032870
    label: cellular response to hormone stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of cellular response to hormone stimulus. HMGCS2 is
      regulated by several hormones (glucagon, insulin, glucocorticoids), so this broad term
      captures regulation of expression rather than the protein's own function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Broad hormone-response term consistent with documented hormonal regulation of the
      ketogenic program; peripheral to catalytic function.
- term:
    id: GO:0033555
    label: multicellular organismal response to stress
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of a very broad organism-level stress-response term.
      Not informative for the enzyme's molecular role.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Overly general organism-level term from automatic ortholog transfer; over-annotation.
- term:
    id: GO:0033574
    label: response to testosterone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to testosterone. Not substantiated for
      HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0033762
    label: response to glucagon
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to glucagon. Glucagon (via cAMP) is a
      principal inducer of hepatic ketogenesis and HMGCS2 transcription during fasting, so
      this annotation reflects a well-established regulatory input.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with glucagon/cAMP induction of ketogenic gene expression during fasting;
      peripheral to the enzyme's catalytic function but biologically grounded.
- term:
    id: GO:0034014
    label: response to triglyceride
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to triglyceride. Not specifically
      supported for HMGCS2's function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0034284
    label: response to monosaccharide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to monosaccharide (e.g., glucose).
      Glucose availability reciprocally regulates ketogenesis, so this is a plausible
      regulatory annotation but peripheral to function.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with glucose/carbohydrate regulation of ketogenic gene expression; non-core.
- term:
    id: GO:0034696
    label: response to prostaglandin F
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to prostaglandin F. Not substantiated
      for HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0042594
    label: response to starvation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to starvation. Fasting/starvation is the
      central physiological trigger for HMGCS2-driven ketogenesis and induces HMGCS2
      expression, so this is among the most biologically relevant of the response-to-X terms.
    action: KEEP_AS_NON_CORE
    reason: >-
      Well-grounded in the fasting physiology of ketogenesis (HMGCS2 is induced during
      starvation), but describes the physiological context rather than the enzyme's molecular
      activity, so it is retained as non-core.
- term:
    id: GO:0043434
    label: response to peptide hormone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to peptide hormone (broad parent of the
      insulin/glucagon responses). Reflects hormonal regulation of ketogenic gene expression.
    action: KEEP_AS_NON_CORE
    reason: >-
      Broad hormone-response term consistent with documented hormonal regulation; non-core.
- term:
    id: GO:0045471
    label: response to ethanol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to ethanol. Not specifically supported
      for HMGCS2's molecular function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0046951
    label: ketone body biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of ketone body biosynthetic process. This is the
      core biological process of HMGCS2 and is independently supported by human IMP and
      Reactome TAS evidence.
    action: ACCEPT
    reason: >-
      Ketone body biosynthesis is the defining physiological role of HMGCS2 (the rate-limiting
      step of ketogenesis). Correct and well-supported; redundant with the IMP/TAS calls.
    supported_by:
    - reference_id: PMID:23751782
      supporting_text: that affects ketone-body synthesis.
- term:
    id: GO:0051384
    label: response to glucocorticoid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to glucocorticoid. Glucocorticoids
      contribute to induction of the fasting/ketogenic program, so this is a plausible
      regulatory annotation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with hormonal (glucocorticoid) regulation of ketogenic gene expression;
      peripheral to catalytic function.
- term:
    id: GO:0051591
    label: response to cAMP
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to cAMP. cAMP is the second messenger of
      glucagon signaling that induces hepatic ketogenesis and HMGCS2 expression, so this term
      reflects a genuine regulatory pathway.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with cAMP/glucagon induction of the ketogenic program; non-core relative to
      the enzyme's activity.
- term:
    id: GO:0060416
    label: response to growth hormone
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to growth hormone. Not specifically
      substantiated for HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0060612
    label: adipose tissue development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of adipose tissue development from the rat ortholog.
      No evidence of a developmental role for HMGCS2 in adipose tissue.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Automatic ortholog transfer that over-annotates a metabolic enzyme with an unrelated
      developmental process.
- term:
    id: GO:0070542
    label: response to fatty acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to fatty acid. Fatty acids (via PPAR-alpha)
      induce the ketogenic program including HMGCS2, so this is a biologically grounded
      regulatory annotation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with fatty-acid/PPAR-alpha induction of HMGCS2 during fasting; peripheral to
      the catalytic function.
- term:
    id: GO:0070543
    label: response to linoleic acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of response to a specific fatty acid (linoleic acid).
      More specific than can be justified for HMGCS2 beyond the general fatty-acid response.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Overly specific ortholog transfer; the general response to fatty acid already captures
      the relevant regulatory input.
- term:
    id: GO:0071222
    label: cellular response to lipopolysaccharide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of cellular response to lipopolysaccharide. Not
      specifically supported for HMGCS2's function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0071230
    label: cellular response to amino acid stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of cellular response to amino acid stimulus. Not
      specifically substantiated for HMGCS2.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Non-specific ortholog phenotype transfer; over-annotation.
- term:
    id: GO:0071385
    label: cellular response to glucocorticoid stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of cellular response to glucocorticoid stimulus.
      Reflects glucocorticoid regulation of the ketogenic program.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with hormonal (glucocorticoid) regulation of HMGCS2 expression; non-core.
- term:
    id: GO:0071398
    label: cellular response to fatty acid
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      Ensembl-Compara electronic transfer of cellular response to fatty acid. Reflects
      fatty-acid/PPAR-alpha induction of the ketogenic program.
    action: KEEP_AS_NON_CORE
    reason: >-
      Consistent with fatty-acid regulation of HMGCS2; peripheral to catalytic function.
- term:
    id: GO:0046951
    label: ketone body biosynthetic process
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77111
  qualifier: involved_in
  review:
    summary: >-
      Reactome traceable-author-statement placing HMGCS2 in the Synthesis of Ketone Bodies
      pathway. This is the core biological process of the enzyme.
    action: ACCEPT
    reason: >-
      Reactome curates HMGCS2 as the enzyme catalyzing the committed step of ketone body
      synthesis, consistent with all experimental and phylogenetic evidence.
    supported_by:
    - reference_id: PMID:23751782
      supporting_text: that affects ketone-body synthesis.
- term:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-73918
  qualifier: enables
  review:
    summary: >-
      Reactome TAS for the HMG-CoA synthase reaction (acetoacetyl-CoA + acetyl-CoA => HMG-CoA
      + CoASH). Core molecular function.
    action: ACCEPT
    reason: >-
      Directly describes the enzyme's catalyzed reaction; consistent with experimental
      evidence and the correct level of specificity.
    supported_by:
    - reference_id: PMID:20346956
      supporting_text: condensation of acetyl-CoA and acetoacetyl-CoA into 3-hydroxy-3-methylglutaryl
- term:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  evidence_type: EXP
  original_reference_id: PMID:11228257
  qualifier: enables
  review:
    summary: >-
      Direct experimental (EXP) evidence for HMG-CoA synthase activity. This study
      characterized wild-type and the F174L disease variant of human mHS by bacterial
      expression and activity assay, establishing the catalytic function.
    action: ACCEPT
    reason: >-
      Experimental characterization of the human enzyme's HMG-CoA synthase activity, with the
      F174L patient variant abolishing detectable activity. This is a definitive, core MF
      annotation.
    supported_by:
    - reference_id: PMID:11228257
      supporting_text: F174L-mHS produces a low level of mHS polypeptide with no detectable activity.
- term:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  evidence_type: EXP
  original_reference_id: PMID:29597274
  qualifier: enables
  review:
    summary: >-
      Direct experimental (EXP) evidence for HMG-CoA synthase activity. This study expressed
      wild-type human mHS and measured its activity relative to numerous disease variants,
      confirming the condensation reaction of ketone body synthesis.
    action: ACCEPT
    reason: >-
      Experimental measurement of human mHS enzymatic activity; core MF annotation supported
      by quantitative enzyme assays.
    supported_by:
    - reference_id: PMID:29597274
      supporting_text: catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      ISS (sequence-similarity) assignment of mitochondrial localization, transferred from the
      rat ortholog P22791. Correct compartment for the mitochondrial isoform bearing an
      N-terminal transit peptide.
    action: ACCEPT
    reason: >-
      Consistent with the mitochondrial transit peptide and matrix localization; redundant
      with the mitochondrion/matrix annotations from other sources.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  qualifier: located_in
  review:
    summary: >-
      High-throughput mass-spectrometry evidence (MitoCoP high-confidence human mitochondrial
      proteome) placing HMGCS2 in mitochondria. Consistent with its established matrix
      localization.
    action: ACCEPT
    reason: >-
      Large-scale proteomic detection in the high-confidence mitochondrial proteome supports
      mitochondrial localization, corroborating the manual/ISS/IBA annotations.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IDA
  original_reference_id: PMID:20346956
  qualifier: enables
  review:
    summary: >-
      IDA annotation of identical protein binding based on the crystal structure of human
      HMGCS2 (PDB 2WYA), which shows the enzyme is a homodimer. The homodimeric assembly is a
      real structural property, but "identical protein binding" is an uninformative molecular
      function term relative to the enzyme's catalytic role.
    action: KEEP_AS_NON_CORE
    reason: >-
      The homodimer is structurally established (self-association is genuine), so per curation
      policy this experimental self-binding annotation is retained rather than removed, but it
      is uninformative about the enzyme's function and is therefore marked non-core.
    supported_by:
    - reference_id: PMID:29597274
      supporting_text: Previous studies have already pointed out that mHS is a homodimeric enzyme
    - reference_id: PMID:29597274
      supporting_text: which was subsequently confirmed by the crystallization of the enzyme
- term:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  evidence_type: IMP
  original_reference_id: PMID:23751782
  qualifier: enables
  review:
    summary: >-
      IMP evidence for HMG-CoA synthase activity: the study developed a method to express
      human mHS and measured the effect of eight disease mutations on catalytic activity,
      demonstrating the enzyme's function through loss-of-activity variants.
    action: ACCEPT
    reason: >-
      Functional analysis of patient mutations (total loss or reduced catalytic efficiency)
      directly demonstrates HMGCS2's HMG-CoA synthase activity. Core MF annotation.
    supported_by:
    - reference_id: PMID:23751782
      supporting_text: an enzyme with a catalytic efficiency of 11.5%.
- term:
    id: GO:0006084
    label: acetyl-CoA metabolic process
  evidence_type: IMP
  original_reference_id: PMID:23751782
  qualifier: involved_in
  review:
    summary: >-
      IMP involvement in acetyl-CoA metabolic process, inferred from mutation analysis of the
      HMG-CoA synthase reaction (which consumes acetyl-CoA). Correct but broad.
    action: ACCEPT
    reason: >-
      Acetyl-CoA is a direct substrate of the reaction assayed in this mutation study; the
      broad metabolic-process term is accurate though non-core relative to ketogenesis.
    supported_by:
    - reference_id: PMID:29597274
      supporting_text: catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
- term:
    id: GO:0046951
    label: ketone body biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:23751782
  qualifier: involved_in
  review:
    summary: >-
      IMP involvement in ketone body biosynthetic process, based on functional analysis of
      disease mutations that impair ketogenesis. This is the core biological process of HMGCS2.
    action: ACCEPT
    reason: >-
      The study links HMGCS2 mutations to a disorder that affects ketone-body synthesis and
      characterizes the associated loss of enzyme activity, directly supporting the ketogenesis
      annotation. Core BP annotation.
    supported_by:
    - reference_id: PMID:23751782
      supporting_text: that affects ketone-body synthesis.
- term:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      ISS assignment of HMG-CoA synthase activity, transferred from the human cytosolic
      paralog HMGCS1 (P54869). Redundant with the experimental evidence for the same term at
      the correct specificity.
    action: ACCEPT
    reason: >-
      The catalytic activity is correct and experimentally established for HMGCS2; the ISS
      transfer converges on the right molecular function despite being based on the paralog.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: EC=2.3.3.10
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1989760
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS for mitochondrial matrix localization (Expression of HMGCS2 pathway). This
      is the precise, correct compartment for the enzyme.
    action: ACCEPT
    reason: >-
      Matrix localization is correct for this matrix-soluble ketogenic enzyme; consistent with
      the transit peptide and other matrix/mitochondrion annotations.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-73918
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS for mitochondrial matrix localization, associated with the HMG-CoA synthase
      reaction. Correct compartment.
    action: ACCEPT
    reason: >-
      Matrix localization corroborated across multiple Reactome events and the transit peptide.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838081
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS for mitochondrial matrix localization, in the context of LONP1-mediated
      degradation of matrix proteins. Correct compartment; annotation reflects HMGCS2 being a
      matrix substrate of the LONP1 quality-control machinery.
    action: ACCEPT
    reason: >-
      The matrix localization is correct. The associated pathway (LONP1 degrades matrix
      proteins) concerns turnover of HMGCS2 rather than its ketogenic function, but the
      cellular-component call is accurate.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9838093
  qualifier: located_in
  review:
    summary: >-
      Reactome TAS for mitochondrial matrix localization, in the context of LONP1 binding
      matrix proteins. Correct compartment.
    action: ACCEPT
    reason: >-
      Matrix localization is accurate; the pathway concerns HMGCS2 as a LONP1 client, not its
      catalytic role, but the compartment annotation is correct.
    supported_by:
    - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Mitochondrion'
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: TAS
  original_reference_id: PMID:7851882
  qualifier: located_in
  review:
    summary: >-
      TAS (from the original human liver mHS cloning paper) for mitochondrial localization.
      The paper established mHS as the first enzyme of ketogenesis, distinct from the cytosolic
      cholesterol-synthesis isozyme, and mitochondrial localization is intrinsic to that
      distinction.
    action: ACCEPT
    reason: >-
      Foundational reference identifying the mitochondrial HMG-CoA synthase; the mitochondrion
      annotation is correct and consistent with all downstream evidence.
    supported_by:
    - reference_id: PMID:7851882
      supporting_text: whereas the cytoplasmic HS isozyme (cHS) mediates an early step
core_functions:
- description: >-
    Catalyzes the committed, rate-limiting step of ketogenesis in the mitochondrial matrix:
    the condensation of acetyl-CoA with acetoacetyl-CoA to form (3S)-3-hydroxy-3-methylglutaryl-CoA
    (HMG-CoA) plus CoA, via an active-site cysteine acyl-thioester intermediate.
  molecular_function:
    id: GO:0004421
    label: hydroxymethylglutaryl-CoA synthase activity
  directly_involved_in:
  - id: GO:0046951
    label: ketone body biosynthetic process
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  supported_by:
  - reference_id: PMID:29597274
    supporting_text: catalyzes the condensation reaction between acetyl-CoA and acetoacetyl-CoA in ketone body synthesis
  - reference_id: file:human/HMGCS2/HMGCS2-uniprot.txt
    supporting_text: Catalyzes the first irreversible step in ketogenesis,
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:11228257
  title: 'Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency: clinical
    course and description of causal mutations in two patients.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Establishes HMGCS2 catalytic activity via bacterial expression of wild-type and the
      F174L disease variant (no detectable activity); supports the EXP MF annotation and the
      disease link. PubMed-verified title/abstract match.
- id: PMID:20346956
  title: Crystal structures of human HMG-CoA synthase isoforms provide insights into
    inherited ketogenesis disorders and inhibitor design.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Crystal structures of the human mitochondrial (HMGCS2) and cytosolic (HMGCS1) isoforms;
      documents the homodimer (supporting identical protein binding) and explicitly separates
      the mitochondrial ketogenic isoform from the cytosolic mevalonate/cholesterol isoform.
- id: PMID:23751782
  title: New case of mitochondrial HMG-CoA synthase deficiency. Functional analysis
    of eight mutations.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Expression/activity assay of eight HMGCS2 disease mutations; supports the IMP MF and
      ketone body biosynthetic process annotations. Abstract-only cached but title/abstract
      verified.
- id: PMID:29597274
  title: 'Human Mitochondrial HMG-CoA Synthase Deficiency: Role of Enzyme Dimerization
    Surface and Characterization of Three New Patients.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text available; expresses and assays wild-type and ten HMGCS2 variants, confirming
      the condensation reaction of ketone body synthesis and the homodimeric nature of mHS.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      Large-scale MitoCoP proteomic study; HMGCS2 is included in the high-confidence human
      mitochondrial proteome (supplementary data), supporting the HTP mitochondrion
      annotation. The protein is not discussed by name in the extracted body text.
- id: PMID:7851882
  title: 'Human mitochondrial HMG CoA synthase: liver cDNA and partial genomic cloning,
    chromosome mapping to 1p12-p13, and possible role in vertebrate evolution.'
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Original cloning of human liver mitochondrial HMG-CoA synthase; identifies mHS as the
      first enzyme of ketogenesis, distinct from the cytoplasmic cholesterol-synthesis isozyme.
      Supports the mitochondrion (TAS) annotation and the HMGCS1/HMGCS2 distinction.
- id: Reactome:R-HSA-1989760
  title: Expression of HMGCS2
  findings: []
- id: Reactome:R-HSA-73918
  title: acetoacetyl-CoA+acetyl-CoA => HMG-CoA + CoASH
  findings: []
- id: Reactome:R-HSA-77111
  title: Synthesis of Ketone Bodies
  findings: []
- id: Reactome:R-HSA-9838081
  title: LONP1 degrades mitochondrial matrix proteins
  findings: []
- id: Reactome:R-HSA-9838093
  title: LONP1 binds mitochondrial matrix proteins
  findings: []
suggested_questions:
- question: >-
    Do the acetylation/succinylation PTMs of HMGCS2 (e.g., at Lys-83/Lys-310) and their reversal
    by SIRT3/SIRT5 provide physiologically significant control of ketogenic flux in human liver,
    beyond transcriptional (PPAR-alpha/FGF21) regulation?
- question: >-
    What, if any, is the function of the muscle/heart-enriched isoform 3 (HMGCS2delta4), and does
    it retain HMG-CoA synthase activity?
suggested_experiments:
- description: >-
    Quantify ketogenic flux (labeled acetyl-CoA to beta-hydroxybutyrate) in primary human
    hepatocytes with HMGCS2 knockdown/knockout versus rescue with wild-type and PTM-site mutants
    to test the contribution of acetylation/succinylation to activity control.
- description: >-
    Express and assay HMGCS2 isoform 3 (HMGCS2delta4) in parallel with isoform 1 to determine
    whether the muscle/heart-enriched splice variant retains catalytic activity or has a distinct
    role.