GLYCTK encodes glycerate kinase, an ATP-dependent enzyme that phosphorylates D-glycerate; curated UniProt and Reactome records describe the product as (2R)-3-phosphoglycerate/3-phospho-D-glycerate. This activity supports metabolism of D-glycerate produced during serine catabolism and minor fructose metabolism and is the affected activity in D-glyceric aciduria. Isoform 1 is cytoplasmic, while isoform 2 has both cytoplasmic and mitochondrial localization; the core gene-level function is glycerate kinase activity rather than protein phosphorylation or generic protein binding.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005737
cytoplasm
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
|
|
GO:0008887
glycerate kinase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
|
|
GO:0000166
nucleotide binding
|
IEA
GO_REF:0000043 |
MARK AS OVER ANNOTATED |
Summary: nucleotide binding is technically compatible with an ATP-dependent kinase but is too broad to add useful information when glycerate kinase activity is already annotated.
Reason: The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term. Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the actual function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: ATP binding is required for the glycerate kinase reaction because ATP is the phosphate donor for conversion of (R)-glycerate to (2R)-3-phosphoglycerate.
Reason: Although less informative than glycerate kinase activity, ATP binding is mechanistically relevant and supported by the catalytic reaction.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+).
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000044 |
KEEP AS NON CORE |
Summary: Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK products.
Reason: Keep this cellular component as a valid non-core localization. The core gene-level location remains cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
|
|
GO:0008887
glycerate kinase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
|
|
GO:0016301
kinase activity
|
IEA
GO_REF:0000043 |
MARK AS OVER ANNOTATED |
Summary: kinase activity is technically compatible with an ATP-dependent kinase but is too broad to add useful information when glycerate kinase activity is already annotated.
Reason: The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term. Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the actual function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
|
|
GO:0016740
transferase activity
|
IEA
GO_REF:0000043 |
MARK AS OVER ANNOTATED |
Summary: transferase activity is technically compatible with an ATP-dependent kinase but is too broad to add useful information when glycerate kinase activity is already annotated.
Reason: The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term. Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the actual function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
|
|
GO:0005515
protein binding
|
IPI
PMID:16189514 Towards a proteome-scale map of the human protein-protein in... |
MARK AS OVER ANNOTATED |
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
|
|
GO:0005515
protein binding
|
IPI
PMID:19060904 An empirical framework for binary interactome mapping. |
MARK AS OVER ANNOTATED |
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
|
|
GO:0005515
protein binding
|
IPI
PMID:25416956 A proteome-scale map of the human interactome network. |
MARK AS OVER ANNOTATED |
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: This generic protein binding row comes from high-throughput interactome evidence and does not describe the biochemical function of GLYCTK.
Reason: Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme. The useful GO annotation is glycerate kinase activity.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
The curated functional annotation describes glycerate kinase catalytic activity, while many listed interactions are high-throughput IntAct records.
|
|
GO:0005829
cytosol
|
IDA
GO_REF:0000052 |
ACCEPT |
Summary: cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
|
|
GO:0061624
fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
|
TAS
Reactome:R-HSA-70350 |
ACCEPT |
Summary: GLYCTK participates in fructose catabolism by phosphorylating D-glycerate, a metabolite generated downstream of fructose metabolism, to 3-phosphoglycerate.
Reason: The Reactome pathway context is appropriate for GLYCTK. The direct molecular function remains glycerate kinase activity, but the biological-process placement in fructose catabolism is supported.
Supporting Evidence:
Reactome:R-HSA-6799495
GLYCTK phosphorylates DGA to 3PDGA
|
|
GO:0008887
glycerate kinase activity
|
EXP
PMID:2537226 D-glycerate kinase deficiency as a cause of D-glyceric acidu... |
ACCEPT |
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
|
|
GO:0005739
mitochondrion
|
HTP
PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... |
KEEP AS NON CORE |
Summary: Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK products.
Reason: Keep this cellular component as a valid non-core localization. The core gene-level location remains cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
|
|
GO:0008887
glycerate kinase activity
|
IDA
PMID:31837836 d-Glycerate kinase deficiency in a neuropediatric patient. |
ACCEPT |
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
|
|
GO:0008887
glycerate kinase activity
|
IMP
PMID:31837836 d-Glycerate kinase deficiency in a neuropediatric patient. |
ACCEPT |
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
|
|
GO:0005829
cytosol
|
TAS
Reactome:R-HSA-6799495 |
ACCEPT |
Summary: cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
|
|
GO:0005737
cytoplasm
|
IDA
PMID:16753811 Isolation and characterization of the human D-glyceric acide... |
ACCEPT |
Summary: cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting as a soluble metabolic enzyme.
Reason: Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform 2, so this is a valid cellular component annotation.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally localized to mitochondria.
|
|
GO:0006468
protein phosphorylation
|
IDA
PMID:16753811 Isolation and characterization of the human D-glyceric acide... |
REMOVE |
Summary: GLYCTK is a small-molecule glycerate kinase, not a protein kinase. Its catalytic activity phosphorylates (R)-glycerate to (2R)-3-phosphoglycerate and does not support protein phosphorylation.
Reason: This is an aspect-correct BP term for protein kinases but a wrong biological-process annotation for GLYCTK. The evidence supports glycerate phosphorylation in metabolism, not phosphorylation of protein substrates.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
|
|
GO:0008887
glycerate kinase activity
|
IDA
PMID:16753811 Isolation and characterization of the human D-glyceric acide... |
ACCEPT |
Summary: glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and human disease reports support loss of this enzyme activity in D-glyceric aciduria.
Reason: This term is specific, aspect-correct, and directly matches the characterized enzyme activity of GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on glycerate kinase activity as the primary molecular function.
Supporting Evidence:
file:human/GLYCTK/GLYCTK-uniprot.txt
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
file:human/GLYCTK/GLYCTK-deep-research-falcon.md
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and links GLYCTK deficiency to D-glyceric aciduria.
|
Q: Which GLYCTK isoforms account for mitochondrial glycerate kinase activity in human tissues?
Suggested experts: metabolic biochemists, mitochondrial proteomics experts
Q: How does GLYCTK deficiency produce variable neurological phenotypes in D-glyceric aciduria?
Suggested experts: clinical geneticists, inborn errors of metabolism specialists
Experiment: Quantitatively compare endogenous GLYCTK isoform 1 and isoform 2 localization in tissues with high fructose or glycerate flux.
Hypothesis: Isoform 2 provides a mitochondrial pool of glycerate kinase activity whereas isoform 1 supports cytosolic glycerate metabolism.
Type: Isoform localization
Experiment: Trace labeled D-glycerate in GLYCTK-null and rescue cells expressing individual isoforms.
Hypothesis: Loss of GLYCTK blocks conversion of D-glycerate into 3-phosphoglycerate and isoform-specific rescue distinguishes cytosolic and mitochondrial contributions.
Type: Metabolic flux analysis
provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-05-03T00:15:53.013659'
end_time: '2026-05-03T00:28:00.684041'
duration_seconds: 727.67
template_file: templates/gene_research_go_focused.md
template_variables:
organism: human
gene_id: GLYCTK
gene_symbol: GLYCTK
uniprot_accession: Q8IVS8
protein_description: 'RecName: Full=Glycerate kinase; EC=2.7.1.31 {ECO:0000269|PubMed:16753811,
ECO:0000269|PubMed:20949620}; AltName: Full=HBeAg-binding protein 4;'
gene_info: Name=GLYCTK; Synonyms=HBEBP4; ORFNames=LP5910;
organism_full: Homo sapiens (Human).
protein_family: Belongs to the glycerate kinase type-2 family.
protein_domains: GK-like_C_sf. (IPR037035); GK_N_sf. (IPR038614); MOFRL. (IPR007835);
MOFRL_assoc_dom. (IPR025286); MOFRL_protein. (IPR039760)
provider_config:
timeout: 600
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citation_count: 21
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'GLYCTK' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene GLYCTK (gene ID: GLYCTK, UniProt: Q8IVS8) in human.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'GLYCTK' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene GLYCTK (gene ID: GLYCTK, UniProt: Q8IVS8) in human.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The UniProt accession Q8IVS8 corresponds to human GLYCTK (synonyms reported in UniProt include HBEBP4), annotated as glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31). The primary human genetics and enzymology literature for D-glyceric aciduria explicitly identifies GLYCTK as encoding D-glycerate 2-kinase and establishes causality between GLYCTK loss-of-function variants and disease, confirming the target identity is correct (sass2010d‐glycericaciduriais pages 12-15, zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2).
GLYCTK (D-glycerate 2-kinase; EC 2.7.1.31) catalyzes phosphorylation of D-glycerate to 2-phosphoglycerate (2-PG) (zehavi2019severeinfantileepileptic pages 1-2). This reaction consumes ATP (kinase reaction; ATP consumption is explicitly described in assay coupling approaches and in mechanistic descriptions linking to glycolytic intermediates) and places GLYCTK at a junction between D-glycerate handling and central carbon metabolism (zehavi2019severeinfantileepileptic pages 1-2, sass2010d‐glycericaciduriais pages 12-15).
Pathway placement: D-glycerate is described as an intermediate metabolite of serine and fructose metabolism, and conversion to 2-phosphoglycerate creates a biochemical link into glycolysis/gluconeogenesis via 2-PG (zehavi2019severeinfantileepileptic pages 1-2, guo2006isolationandcharacterization pages 4-5).
D-glyceric aciduria (OMIM #220120) is an autosomal recessive inborn error of metabolism caused by mutations in GLYCTK, leading to accumulation of D-glycerate in tissues and massive urinary excretion (zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2). Clinically, DGA is often framed as a disorder linked to serine and fructose metabolism (swanson2017dglycericaciduriadoes pages 1-2, sass2020dglyceratekinasedeficiency pages 1-2).
The disease and enzymology evidence in the retrieved primary literature specifically centers on D-glycerate as the physiological substrate, with formation of 2-phosphoglycerate as the product (zehavi2019severeinfantileepileptic pages 1-2, sass2010d‐glycericaciduriais pages 12-15). The available extracted evidence does not provide a broader substrate panel; thus, substrate specificity beyond D-glycerate cannot be asserted from the retrieved texts.
A core functional validation study expressed reference human GLYCTK cDNA in HEK293 cells, showing:
- Enzyme activity increased from trace amounts (<0.5 µmol·min⁻¹·g⁻¹ protein) in controls to 30.7 µmol·min⁻¹·g⁻¹ protein after expression of reference GLYCTK (sass2010d‐glycericaciduriais pages 12-15).
- The measured Km for D-glycerate was 0.1 mM (mean of two transfection series) (sass2010d‐glycericaciduriais pages 12-15).
- Patient-derived mutant forms (frameshift or missense) produced no enhanced protein signal and no detectable activity in this expression system (sass2010d‐glycericaciduriais pages 12-15).
Figure-based support for the activity comparison (reference vs mutants) is available as a cropped figure from the paper (sass2010d‐glycericaciduriais media 5f02c9bb).
A cloning/characterization study identified two alternatively spliced transcripts, GLYCTK1 and GLYCTK2, and used GFP-fusion experiments in mammalian cells to assess localization:
- Both isoforms were reported as cytosolic (particulate).
- GLYCTK2 was additionally reported to be specifically localized to mitochondria, whereas GLYCTK1 was not (guo2006isolationandcharacterization pages 4-5).
These findings support the concept that GLYCTK function can occur in both cytosolic and mitochondrial compartments, with mitochondrial targeting being isoform-dependent (guo2006isolationandcharacterization pages 4-5).
Both transcript variants were detected by RT-PCR across a broad panel of 17 human tissues, indicating widespread expression (guo2006isolationandcharacterization pages 1-4). Mouse in situ hybridization also showed notable expression in neural regions and skeletal muscle (guo2006isolationandcharacterization pages 4-5, guo2006isolationandcharacterization pages 5-6), which has been interpreted as consistent with neurological involvement in severe cases (guo2006isolationandcharacterization pages 5-6).
A key human mutation/functional paper reported homozygous exon 5 GLYCTK variants in unrelated DGA patients and functionally demonstrated loss of enzyme activity upon expression of the mutant alleles (sass2010d‐glycericaciduriais pages 12-15). This provides direct experimental support that GLYCTK is the causative gene for DGA in these cases.
Pathogenic GLYCTK variants reported across retrieved studies include:
- c.1448delT (p.Phe483SerfsX2) (sass2010d‐glycericaciduriais pages 12-15, swanson2017dglycericaciduriadoes pages 1-2)
- c.1478T>G (p.Phe493Cys) (sass2010d‐glycericaciduriais pages 12-15)
- c.1558delC (p.Leu520CysfsX108) (sass2010d‐glycericaciduriais pages 12-15)
- c.455T>C (p.Leu152Pro) (zehavi2019severeinfantileepileptic pages 1-2)
- c.517G>T (p.Val173Leu) (sass2020dglyceratekinasedeficiency pages 1-2)
In DGA patients with GLYCTK deficiency, quantitative elevations reported include:
- Plasma D-glycerate 1.0–1.3 mM (historical patient A; normal reported as not detectable) (sass2010d‐glycericaciduriais pages 12-15).
- Urinary glycerate reported as 9.32 mol/mol creatinine (patient B) and 11.3, 8.61, 18.6 mol/mol creatinine (three samples from patient C) (sass2010d‐glycericaciduriais pages 12-15).
- Serum glycerate 1 mM (patient C) (sass2010d‐glycericaciduriais pages 12-15).
These values provide concrete biochemical anchors for functional annotation and diagnostic expectations.
The phenotype spectrum is repeatedly described as highly variable, ranging from severe progressive infantile encephalopathy to mild/nearly asymptomatic presentations (zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2).
Across case-based summaries in the retrieved literature:
- A review/case report describes 15 previously reported patients plus the current case (total 16) and emphasizes severe neurological impairment in many cases (zehavi2019severeinfantileepileptic pages 1-2).
- Another neuropediatric case report notes that 16 individuals had been described with tentative diagnosis, but only six had prior mutation confirmation, and presents the seventh genetically confirmed case (sass2020dglyceratekinasedeficiency pages 1-2).
Severe neurologic manifestations reported in a progressive case include profound psychomotor retardation, progressive microcephaly, intractable seizures, cortical blindness and deafness, hypotonia progressing to spasticity, progressive brain atrophy on MRI, and death at 9.5 years following status epilepticus (zehavi2019severeinfantileepileptic pages 1-2). A milder neuropediatric case includes severe early hypotonia, hypermobility, tremor, delayed milestones, and diffuse slow EEG background without a specific epileptic syndrome (sass2020dglyceratekinasedeficiency pages 1-2).
Within the tool-retrieved set, no 2023–2024 primary mechanistic papers focused specifically on human GLYCTK enzymology, structure, or cell biology were accessible. The most informative GLYCTK functional/disease evidence available here remains from foundational studies (2006–2020) (sass2010d‐glycericaciduriais pages 12-15, guo2006isolationandcharacterization pages 4-5, zehavi2019severeinfantileepileptic pages 1-2, sass2020dglyceratekinasedeficiency pages 1-2).
Two 2023–2024 papers retrieved are primarily platform/resource contributions rather than GLYCTK biology:
- SpliceProt 2.0 (published 18 Jan 2024) is a proteogenomics repository aimed at cataloging proteoforms; it is relevant indirectly for splice-variant-aware proteomics workflows, but does not provide GLYCTK-specific functional data in the retrieved sections (santos2024spliceprot2.0a pages 1-2, santos2024spliceprot2.0a pages 2-4).
- Metaboverse (published Apr 2023) is a computational tool for metabolic network visualization and pattern discovery; the retrieved excerpt does not provide GLYCTK-specific biology beyond general metabolic-network context (berg2023metaboverseenablesautomated pages 8-9, berg2023metaboverseenablesautomated pages 9-10).
Real-world implementation of GLYCTK knowledge is primarily in metabolic diagnostics:
- Urine organic acid analysis detects elevated glycerate; subsequent enantioselective analysis can distinguish D- vs L-glycerate to differentiate DGA (GLYCTK deficiency) from primary hyperoxaluria type 2 (L-glycerate) (sass2020dglyceratekinasedeficiency pages 1-2, zehavi2019severeinfantileepileptic pages 1-2).
- Genetic testing (GLYCTK sequencing) provides confirmatory diagnosis and can resolve confounded historical diagnoses (e.g., co-occurring disorders) (swanson2017dglycericaciduriadoes pages 1-2, sass2010d‐glycericaciduriais pages 12-15).
The HEK293 overexpression assay provides an implemented approach for functional validation of candidate GLYCTK variants, demonstrating that disease-associated alleles can abolish detectable activity/protein (sass2010d‐glycericaciduriais pages 12-15, sass2010d‐glycericaciduriais media 5f02c9bb).
Authors emphasize that clinical expressivity is broad, including families with asymptomatic affected siblings, raising the possibility of ascertainment bias and/or modifying factors (swanson2017dglycericaciduriadoes pages 1-2). This complicates straightforward genotype–phenotype mapping.
Although GLYCTK is primarily discussed as an enzyme in serine/fructose metabolism, authors have speculated that in higher animals glycerate kinase may have roles in neural systems and cell differentiation (guo2006isolationandcharacterization pages 6-7). A neuropediatric case report explicitly suggests future work should search for additional roles beyond catabolism of serine and fructose (sass2020dglyceratekinasedeficiency pages 1-2). These are hypotheses/opinions rather than demonstrated mechanisms in the extracted evidence.
OpenTargets reports a GLYCTK association with D-glyceric aciduria (MONDO_0009070) supported by multiple evidence entries and PubMed links, consistent with the primary literature linking GLYCTK mutations to DGA (sass2010d‐glycericaciduriais pages 12-15).
The following table consolidates the key functional annotation points extracted from the retrieved literature.
| Claim/Topic | Key evidence (short) | Source (authors year journal) | URL | Publication date | Citation ID |
|---|---|---|---|---|---|
| Reaction | Human GLYCTK encodes D-glycerate 2-kinase (EC 2.7.1.31), converting D-glycerate to 2-phosphoglycerate; D-glycerate is an intermediate of serine and fructose metabolism. | Zehavi et al. 2019, Metabolic Brain Disease | https://doi.org/10.1007/s11011-019-0384-x | 2019-01-12 | (zehavi2019severeinfantileepileptic pages 1-2) |
| Km | Recombinant human GLYCTK expressed in HEK293 homogenates had a reported Km for D-glycerate of 0.1 mM (mean of two transfection series). | Sass et al. 2010, Human Mutation | https://doi.org/10.1002/humu.21375 | 2010-12 | (sass2010d‐glycericaciduriais pages 12-15) |
| Activity | Transfection with reference GLYCTK increased enzyme activity from trace amounts (<0.5 µmol min-1 g-1 protein) to 30.7 µmol min-1 g-1 protein in HEK293 cells. | Sass et al. 2010, Human Mutation | https://doi.org/10.1002/humu.21375 | 2010-12 | (sass2010d‐glycericaciduriais pages 12-15) |
| Localization / splice variants | Two splice variants were cloned: GLYCTK1 and GLYCTK2. Both were reported as cytosolic, and GLYCTK2 was specifically localized to mitochondria; both transcripts were widely expressed across 17 human tissues. | Guo et al. 2006, DNA Sequence | https://doi.org/10.1080/10425170500476665 | 2006-01 | (guo2006isolationandcharacterization pages 1-4, guo2006isolationandcharacterization pages 4-5) |
| Disease association | GLYCTK deficiency causes D-glyceric aciduria, a rare autosomal recessive inborn error of metabolism with isolated accumulation of the D-enantiomer of glyceric acid. | Sass et al. 2020, Brain and Development | https://doi.org/10.1016/j.braindev.2019.11.008 | 2020-02 | (sass2020dglyceratekinasedeficiency pages 1-2) |
| Mutations | Pathogenic variants reported include c.1448delT (p.Phe483SerfsX2), c.1478T>G (p.Phe493Cys), c.1558delC (p.Leu520CysfsX108), c.455T>C (p.Leu152Pro), and c.517G>T (p.Val173Leu). Mutant forms tested in HEK293 cells showed no enhanced protein signal or activity. | Sass et al. 2010, Human Mutation; Zehavi et al. 2019, Metabolic Brain Disease; Sass et al. 2020, Brain and Development | https://doi.org/10.1002/humu.21375 ; https://doi.org/10.1007/s11011-019-0384-x ; https://doi.org/10.1016/j.braindev.2019.11.008 | 2010-12; 2019-01-12; 2020-02 | (sass2010d‐glycericaciduriais pages 12-15, zehavi2019severeinfantileepileptic pages 1-2, sass2020dglyceratekinasedeficiency pages 1-2) |
| Phenotype variability | Clinical spectrum is highly variable, ranging from severe progressive infantile encephalopathy with intractable seizures, cortical blindness and deafness to mild neurologic dysfunction or practically asymptomatic cases. | Zehavi et al. 2019, Metabolic Brain Disease; Swanson et al. 2017, Molecular Genetics and Metabolism | https://doi.org/10.1007/s11011-019-0384-x ; https://doi.org/10.1016/j.ymgme.2017.04.009 | 2019-01-12; 2017-06 | (zehavi2019severeinfantileepileptic pages 1-2, swanson2017dglycericaciduriadoes pages 1-2) |
| Quantitative metabolite data | Patient A plasma D-glycerate 1.0-1.3 mM; patient B urinary glycerate 9.32 mol/mol creatinine; patient C urinary glycerate 11.3, 8.61, and 18.6 mol/mol creatinine; patient C serum glycerate 1 mM. | Sass et al. 2010, Human Mutation | https://doi.org/10.1002/humu.21375 | 2010-12 | (sass2010d‐glycericaciduriais pages 12-15) |
| Case count / genetically confirmed cases | About 16 individuals with tentative diagnosis had been described by 2020, with only six previously genetically confirmed; the 2020 report was the seventh genetically confirmed case. | Sass et al. 2020, Brain and Development | https://doi.org/10.1016/j.braindev.2019.11.008 | 2020-02 | (sass2020dglyceratekinasedeficiency pages 1-2) |
Table: This table summarizes the key functional annotation evidence for human GLYCTK/Q8IVS8 from the provided literature context, covering enzymatic function, localization, disease association, mutations, phenotype spectrum, and quantitative data.
References
(sass2010d‐glycericaciduriais pages 12-15): Jörn Oliver Sass, Kathleen Fischer, Raymond Wang, Ernst Christensen, Sabine Scholl-Bürgi, Richard Chang, Klaus Kapelari, and Melanie Walter. D‐glyceric aciduria is caused by genetic deficiency of d‐glycerate kinase (glyctk). Human Mutation, 31:1280-1285, Dec 2010. URL: https://doi.org/10.1002/humu.21375, doi:10.1002/humu.21375. This article has 36 citations and is from a domain leading peer-reviewed journal.
(zehavi2019severeinfantileepileptic pages 1-2): Yoav Zehavi, Hanna Mandel, Ayelet Eran, Sarit Ravid, Muhammad Abu Rashid, Erwin E. W. Jansen, Mirjam M. C. Wamelink, Ann Saada, Avraham Shaag, Orly Elpeleg, and Ronen Spiegel. Severe infantile epileptic encephalopathy associated with d-glyceric aciduria: report of a novel case and review. Metabolic Brain Disease, 34:557-563, Jan 2019. URL: https://doi.org/10.1007/s11011-019-0384-x, doi:10.1007/s11011-019-0384-x. This article has 11 citations and is from a peer-reviewed journal.
(swanson2017dglycericaciduriadoes pages 1-2): Michael A. Swanson, Stephanie M. Garcia, Elaine Spector, Kathryn Kronquist, Geralyn Creadon-Swindell, Melanie Walter, Ernst Christensen, Johan L.K. Van Hove, and Jörn Oliver Sass. D-glyceric aciduria does not cause nonketotic hyperglycinemia: a historic co-occurrence. Molecular Genetics and Metabolism, 121:80-82, Jun 2017. URL: https://doi.org/10.1016/j.ymgme.2017.04.009, doi:10.1016/j.ymgme.2017.04.009. This article has 12 citations and is from a peer-reviewed journal.
(guo2006isolationandcharacterization pages 4-5): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.
(sass2020dglyceratekinasedeficiency pages 1-2): Jörn Oliver Sass, Sidney Behringer, Malkanthi Fernando, Elisabetta Cesaroni, Ida Cursio, Alberto Volpini, and Claudia Till. D-glycerate kinase deficiency in a neuropediatric patient. Brain and Development, 42:226-230, Feb 2020. URL: https://doi.org/10.1016/j.braindev.2019.11.008, doi:10.1016/j.braindev.2019.11.008. This article has 9 citations and is from a peer-reviewed journal.
(sass2010d‐glycericaciduriais media 5f02c9bb): Jörn Oliver Sass, Kathleen Fischer, Raymond Wang, Ernst Christensen, Sabine Scholl-Bürgi, Richard Chang, Klaus Kapelari, and Melanie Walter. D‐glyceric aciduria is caused by genetic deficiency of d‐glycerate kinase (glyctk). Human Mutation, 31:1280-1285, Dec 2010. URL: https://doi.org/10.1002/humu.21375, doi:10.1002/humu.21375. This article has 36 citations and is from a domain leading peer-reviewed journal.
(guo2006isolationandcharacterization pages 1-4): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.
(guo2006isolationandcharacterization pages 5-6): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.
(santos2024spliceprot2.0a pages 1-2): Letícia Graziela Costa Santos, Vinícius da Silva Coutinho Parreira, Esdras Matheus Gomes da Silva, Marlon Dias Mariano Santos, Alexander da Franca Fernandes, Ana Gisele da Costa Neves-Ferreira, Paulo Costa Carvalho, Flávia Cristina de Paula Freitas, and Fabio Passetti. Spliceprot 2.0: a sequence repository of human, mouse, and rat proteoforms. International Journal of Molecular Sciences, 25:1183, Jan 2024. URL: https://doi.org/10.3390/ijms25021183, doi:10.3390/ijms25021183. This article has 2 citations.
(santos2024spliceprot2.0a pages 2-4): Letícia Graziela Costa Santos, Vinícius da Silva Coutinho Parreira, Esdras Matheus Gomes da Silva, Marlon Dias Mariano Santos, Alexander da Franca Fernandes, Ana Gisele da Costa Neves-Ferreira, Paulo Costa Carvalho, Flávia Cristina de Paula Freitas, and Fabio Passetti. Spliceprot 2.0: a sequence repository of human, mouse, and rat proteoforms. International Journal of Molecular Sciences, 25:1183, Jan 2024. URL: https://doi.org/10.3390/ijms25021183, doi:10.3390/ijms25021183. This article has 2 citations.
(berg2023metaboverseenablesautomated pages 8-9): Jordan A. Berg, Youjia Zhou, Yeyun Ouyang, Ahmad A. Cluntun, T. Cameron Waller, Megan E. Conway, Sara M. Nowinski, Tyler Van Ry, Ian George, James E. Cox, Bei Wang, and Jared Rutter. Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns. Nature Cell Biology, 25:616-625, Apr 2023. URL: https://doi.org/10.1038/s41556-023-01117-9, doi:10.1038/s41556-023-01117-9. This article has 12 citations and is from a highest quality peer-reviewed journal.
(berg2023metaboverseenablesautomated pages 9-10): Jordan A. Berg, Youjia Zhou, Yeyun Ouyang, Ahmad A. Cluntun, T. Cameron Waller, Megan E. Conway, Sara M. Nowinski, Tyler Van Ry, Ian George, James E. Cox, Bei Wang, and Jared Rutter. Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns. Nature Cell Biology, 25:616-625, Apr 2023. URL: https://doi.org/10.1038/s41556-023-01117-9, doi:10.1038/s41556-023-01117-9. This article has 12 citations and is from a highest quality peer-reviewed journal.
(guo2006isolationandcharacterization pages 6-7): Jin-Hu Guo, Saiyin Hexige, Li Chen, Guang-Jin Zhou, Xiang Wang, Jian-Min Jiang, Ya-Hui Kong, Guo-Qing Ji, Chao-Qun Wu, Shou-Yuan Zhao, and Long Yu. Isolation and characterization of the human d-glyceric acidemia related glycerate kinase gene glyctk1 and its alternatively splicing variant glyctk2. DNA Sequence, 17:1-7, Jan 2006. URL: https://doi.org/10.1080/10425170500476665, doi:10.1080/10425170500476665. This article has 19 citations.
id: Q8IVS8
gene_symbol: GLYCTK
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
GLYCTK encodes glycerate kinase, an ATP-dependent enzyme that phosphorylates D-glycerate; curated UniProt
and Reactome records describe the product as (2R)-3-phosphoglycerate/3-phospho-D-glycerate. This activity
supports metabolism of D-glycerate produced during serine catabolism and minor fructose metabolism and
is the affected activity in D-glyceric aciduria. Isoform 1 is cytoplasmic, while isoform 2 has both
cytoplasmic and mitochondrial localization; the core gene-level function is glycerate kinase activity
rather than protein phosphorylation or generic protein binding.
existing_annotations:
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting
as a soluble metabolic enzyme.
action: ACCEPT
reason: >-
Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
2, so this is a valid cellular component annotation.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
localized to mitochondria.
- term:
id: GO:0008887
label: glycerate kinase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
human disease reports support loss of this enzyme activity in D-glyceric aciduria.
action: ACCEPT
reason: >-
This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
glycerate kinase activity as the primary molecular function.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
links GLYCTK deficiency to D-glyceric aciduria.
- term:
id: GO:0000166
label: nucleotide binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
nucleotide binding is technically compatible with an ATP-dependent kinase but is too broad to add
useful information when glycerate kinase activity is already annotated.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term.
Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the
actual function.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
- term:
id: GO:0005524
label: ATP binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
ATP binding is required for the glycerate kinase reaction because ATP is the phosphate donor for
conversion of (R)-glycerate to (2R)-3-phosphoglycerate.
action: ACCEPT
reason: >-
Although less informative than glycerate kinase activity, ATP binding is mechanistically relevant
and supported by the catalytic reaction.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+).
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting
as a soluble metabolic enzyme.
action: ACCEPT
reason: >-
Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
2, so this is a valid cellular component annotation.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
localized to mitochondria.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial
proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK
products.
action: KEEP_AS_NON_CORE
reason: >-
Keep this cellular component as a valid non-core localization. The core gene-level location remains
cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
localized to mitochondria.
- term:
id: GO:0008887
label: glycerate kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
human disease reports support loss of this enzyme activity in D-glyceric aciduria.
action: ACCEPT
reason: >-
This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
glycerate kinase activity as the primary molecular function.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
links GLYCTK deficiency to D-glyceric aciduria.
- term:
id: GO:0016301
label: kinase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
kinase activity is technically compatible with an ATP-dependent kinase but is too broad to add useful
information when glycerate kinase activity is already annotated.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term.
Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the
actual function.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
- term:
id: GO:0016740
label: transferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
transferase activity is technically compatible with an ATP-dependent kinase but is too broad to
add useful information when glycerate kinase activity is already annotated.
action: MARK_AS_OVER_ANNOTATED
reason: >-
The annotation should be interpreted through the specific GO:0008887 glycerate kinase activity term.
Broad parent terms such as nucleotide binding, kinase activity, and transferase activity blur the
actual function.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
GLYCTK is annotated with the specific catalytic reaction for glycerate kinase activity, EC=2.7.1.31.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:16189514
review:
summary: >-
This generic protein binding row comes from high-throughput interactome evidence and does not describe
the biochemical function of GLYCTK.
action: MARK_AS_OVER_ANNOTATED
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
The curated functional annotation describes glycerate kinase catalytic activity, while many listed
interactions are high-throughput IntAct records.
reason: >-
Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
The useful GO annotation is glycerate kinase activity.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:19060904
review:
summary: >-
This generic protein binding row comes from high-throughput interactome evidence and does not describe
the biochemical function of GLYCTK.
action: MARK_AS_OVER_ANNOTATED
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
The curated functional annotation describes glycerate kinase catalytic activity, while many listed
interactions are high-throughput IntAct records.
reason: >-
Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
The useful GO annotation is glycerate kinase activity.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:25416956
review:
summary: >-
This generic protein binding row comes from high-throughput interactome evidence and does not describe
the biochemical function of GLYCTK.
action: MARK_AS_OVER_ANNOTATED
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
The curated functional annotation describes glycerate kinase catalytic activity, while many listed
interactions are high-throughput IntAct records.
reason: >-
Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
The useful GO annotation is glycerate kinase activity.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
review:
summary: >-
This generic protein binding row comes from high-throughput interactome evidence and does not describe
the biochemical function of GLYCTK.
action: MARK_AS_OVER_ANNOTATED
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
The curated functional annotation describes glycerate kinase catalytic activity, while many listed
interactions are high-throughput IntAct records.
reason: >-
Protein binding is uninformative here and is not the core molecular role of this metabolic enzyme.
The useful GO annotation is glycerate kinase activity.
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: GO_REF:0000052
review:
summary: >-
cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as
a soluble metabolic enzyme.
action: ACCEPT
reason: >-
Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
2, so this is a valid cellular component annotation.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
localized to mitochondria.
- term:
id: GO:0061624
label: fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
evidence_type: TAS
original_reference_id: Reactome:R-HSA-70350
review:
summary: >-
GLYCTK participates in fructose catabolism by phosphorylating D-glycerate, a metabolite generated
downstream of fructose metabolism, to 3-phosphoglycerate.
action: ACCEPT
reason: >-
The Reactome pathway context is appropriate for GLYCTK. The direct molecular function remains glycerate
kinase activity, but the biological-process placement in fructose catabolism is supported.
supported_by:
- reference_id: Reactome:R-HSA-6799495
supporting_text: >-
GLYCTK phosphorylates DGA to 3PDGA
- term:
id: GO:0008887
label: glycerate kinase activity
evidence_type: EXP
original_reference_id: PMID:2537226
review:
summary: >-
glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
human disease reports support loss of this enzyme activity in D-glyceric aciduria.
action: ACCEPT
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
links GLYCTK deficiency to D-glyceric aciduria.
reason: >-
This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
glycerate kinase activity as the primary molecular function.
- term:
id: GO:0005739
label: mitochondrion
evidence_type: HTP
original_reference_id: PMID:34800366
review:
summary: >-
Mitochondrial localization is supported for GLYCTK isoform 2 and by high-throughput mitochondrial
proteomics, but it is isoform/context-specific rather than the universal location of all GLYCTK
products.
action: KEEP_AS_NON_CORE
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: [Isoform 2]: Cytoplasm. Mitochondrion.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
localized to mitochondria.
reason: >-
Keep this cellular component as a valid non-core localization. The core gene-level location remains
cytoplasm/cytosol, with mitochondrion applying to isoform 2 and proteomic detections.
- term:
id: GO:0008887
label: glycerate kinase activity
evidence_type: IDA
original_reference_id: PMID:31837836
review:
summary: >-
glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
human disease reports support loss of this enzyme activity in D-glyceric aciduria.
action: ACCEPT
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
links GLYCTK deficiency to D-glyceric aciduria.
reason: >-
This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
glycerate kinase activity as the primary molecular function.
- term:
id: GO:0008887
label: glycerate kinase activity
evidence_type: IMP
original_reference_id: PMID:31837836
review:
summary: >-
glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
human disease reports support loss of this enzyme activity in D-glyceric aciduria.
action: ACCEPT
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
links GLYCTK deficiency to D-glyceric aciduria.
reason: >-
This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
glycerate kinase activity as the primary molecular function.
- term:
id: GO:0005829
label: cytosol
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6799495
review:
summary: >-
cytosol localization is consistent with the UniProt isoform annotation and with GLYCTK acting as
a soluble metabolic enzyme.
action: ACCEPT
reason: >-
Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
2, so this is a valid cellular component annotation.
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
localized to mitochondria.
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IDA
original_reference_id: PMID:16753811
review:
summary: >-
cytoplasm localization is consistent with the UniProt isoform annotation and with GLYCTK acting
as a soluble metabolic enzyme.
action: ACCEPT
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
SUBCELLULAR LOCATION: [Isoform 1]: Cytoplasm. [Isoform 2]: Cytoplasm. Mitochondrion.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report summarizes that GLYCTK1 and GLYCTK2 were reported as cytosolic, with GLYCTK2 additionally
localized to mitochondria.
reason: >-
Cytoplasmic/cytosolic localization is directly supported for isoform 1 and also applies to isoform
2, so this is a valid cellular component annotation.
- term:
id: GO:0006468
label: protein phosphorylation
evidence_type: IDA
original_reference_id: PMID:16753811
review:
summary: >-
GLYCTK is a small-molecule glycerate kinase, not a protein kinase. Its catalytic activity phosphorylates
(R)-glycerate to (2R)-3-phosphoglycerate and does not support protein phosphorylation.
action: REMOVE
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
reason: >-
This is an aspect-correct BP term for protein kinases but a wrong biological-process annotation
for GLYCTK. The evidence supports glycerate phosphorylation in metabolism, not phosphorylation of
protein substrates.
- term:
id: GO:0008887
label: glycerate kinase activity
evidence_type: IDA
original_reference_id: PMID:16753811
review:
summary: >-
glycerate kinase activity is the specific core molecular function of GLYCTK. The UniProt catalytic
activity describes ATP-dependent phosphorylation of (R)-glycerate to (2R)-3-phosphoglycerate, and
human disease reports support loss of this enzyme activity in D-glyceric aciduria.
action: ACCEPT
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
links GLYCTK deficiency to D-glyceric aciduria.
reason: >-
This term is specific, aspect-correct, and directly matches the characterized enzyme activity of
GLYCTK. Experimental, phylogenetic, computational, and mutant-phenotype evidence all converge on
glycerate kinase activity as the primary molecular function.
references:
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary
mapping, accompanied by conservative changes to GO terms applied by UniProt
findings: []
- id: GO_REF:0000052
title: Gene Ontology annotation based on curation of immunofluorescence data
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:16189514
title: Towards a proteome-scale map of the human protein-protein interaction network.
findings: []
- id: PMID:16753811
title: Isolation and characterization of the human D-glyceric acidemia related glycerate kinase
gene GLYCTK1 and its alternatively splicing variant GLYCTK2.
findings: []
- id: PMID:19060904
title: An empirical framework for binary interactome mapping.
findings: []
- id: PMID:2537226
title: D-glycerate kinase deficiency as a cause of D-glyceric aciduria.
findings: []
- id: PMID:25416956
title: A proteome-scale map of the human interactome network.
findings: []
- id: PMID:31837836
title: d-Glycerate kinase deficiency in a neuropediatric patient.
findings: []
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings: []
- id: PMID:34800366
title: Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular
context.
findings: []
- id: Reactome:R-HSA-6799495
title: GLYCTK phosphorylates DGA to 3PDGA
findings: []
- id: Reactome:R-HSA-70350
title: Fructose catabolism
findings: []
- id: file:human/GLYCTK/GLYCTK-uniprot.txt
title: UniProt record for human GLYCTK
findings: []
- id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
title: Falcon deep research on GLYCTK function
findings:
- statement: Falcon report confirms GLYCTK identity as human glycerate kinase/EC 2.7.1.31 and
summarizes D-glyceric aciduria evidence.
supporting_text: >-
The UniProt accession Q8IVS8 corresponds to human GLYCTK, annotated as glycerate kinase / D-glycerate
2-kinase (EC 2.7.1.31).
- statement: Falcon report summarizes isoform-dependent cytosolic and mitochondrial localization.
supporting_text: >-
Both isoforms were reported as cytosolic (particulate). GLYCTK2 was additionally reported to be
specifically localized to mitochondria, whereas GLYCTK1 was not.
core_functions:
- description: >-
Phosphorylates D-glycerate using ATP, providing the core enzymatic step for D-glycerate metabolism
in serine/fructose catabolic context; UniProt and Reactome describe the product as (2R)-3-phosphoglycerate/3-phospho-D-glycerate.
molecular_function:
id: GO:0008887
label: glycerate kinase activity
directly_involved_in:
- id: GO:0061624
label: fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate
locations:
- id: GO:0005829
label: cytosol
substrates:
- id: CHEBI:16659
label: (R)-glycerate
supported_by:
- reference_id: file:human/GLYCTK/GLYCTK-uniprot.txt
supporting_text: >-
Reaction=(R)-glycerate + ATP = (2R)-3-phosphoglycerate + ADP + H(+); EC=2.7.1.31.
- reference_id: file:human/GLYCTK/GLYCTK-deep-research-falcon.md
supporting_text: >-
Falcon report confirms GLYCTK as human glycerate kinase / D-glycerate 2-kinase (EC 2.7.1.31) and
emphasizes D-glycerate as the physiological substrate.
proposed_new_terms: []
suggested_questions:
- question: Which GLYCTK isoforms account for mitochondrial glycerate kinase activity in human
tissues?
experts:
- metabolic biochemists
- mitochondrial proteomics experts
- question: How does GLYCTK deficiency produce variable neurological phenotypes in D-glyceric
aciduria?
experts:
- clinical geneticists
- inborn errors of metabolism specialists
suggested_experiments:
- experiment_type: Isoform localization
description: Quantitatively compare endogenous GLYCTK isoform 1 and isoform 2 localization in
tissues with high fructose or glycerate flux.
hypothesis: Isoform 2 provides a mitochondrial pool of glycerate kinase activity whereas isoform 1
supports cytosolic glycerate metabolism.
- experiment_type: Metabolic flux analysis
description: Trace labeled D-glycerate in GLYCTK-null and rescue cells expressing individual
isoforms.
hypothesis: Loss of GLYCTK blocks conversion of D-glycerate into 3-phosphoglycerate and
isoform-specific rescue distinguishes cytosolic and mitochondrial contributions.