DPM3

UniProt ID: Q9P2X0
Organism: Homo sapiens
Review Status: INITIALIZED
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Gene Description

DPM3 is the small (92-residue) membrane-anchoring and stabilizer subunit of the heterotrimeric dolichol-phosphate mannose (Dol-P-Man / DPM) synthase complex, which also comprises the catalytic subunit DPM1 and the regulatory subunit DPM2. DPM synthase transfers mannose from cytosolic GDP-mannose to dolichyl phosphate at the endoplasmic reticulum membrane to produce dolichol-phosphate-mannose (Dol-P-Man), the essential lumenal mannosyl donor for GPI-anchor biosynthesis, N-glycan precursor assembly, and protein O- and C-mannosylation. DPM3 is non-catalytic; because the catalytic DPM1 subunit lacks a transmembrane domain, DPM3 (a multi-pass ER membrane protein) tethers DPM1 to the ER membrane and bridges the complex, associating with DPM1 through its C-terminal region and with DPM2 through its N-terminal region. This scaffolding stabilizes DPM1 and is required for assembly and activity of the DPM synthase. Loss of DPM3 function causes DPM3-CDG, an alpha-dystroglycanopathy-type congenital muscular dystrophy (with elevated serum creatine kinase, reduced O-mannosylation of alpha-dystroglycan, and cardiomyopathy in some patients).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005789 endoplasmic reticulum membrane
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) localization of DPM3 to the ER membrane, where the DPM synthase complex acts. This is consistent with the experimentally determined localization and with DPM3 being a multi-pass ER membrane protein.
Reason: The ER membrane is the established site of the DPM synthase complex and of DPM3, corroborated by IDA localization and the UniProt subcellular location.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) involvement in dolichol-linked oligosaccharide biosynthesis. DPM synthase produces Dol-P-Man, the mannosyl donor consumed during assembly of the dolichol-linked oligosaccharide (N-glycan precursor), so DPM3 contributes to this process as part of the complex.
Reason: DPM3 is required for DPM synthase activity, which supplies the Dol-P-Man mannosyl donor used in dolichol-linked oligosaccharide (LLO) assembly and downstream glycosylation.
Supporting Evidence:
PMID:10835346
N-glycan and protein O- and C-mannosylation.
GO:0033185 dolichol-phosphate-mannose synthase complex
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) assignment of DPM3 as part of the dolichol-phosphate-mannose synthase complex. This is the defining complex membership of DPM3 and is strongly supported experimentally.
Reason: DPM3 is one of the three subunits (DPM1/DPM2/DPM3) of the human DPM synthase complex; complex membership is directly established experimentally.
Supporting Evidence:
PMID:10835346
The third subunit, DPM3, comprises 92 amino acids associated with DPM1
GO:0005789 endoplasmic reticulum membrane
IEA
GO_REF:0000044
ACCEPT
Summary: Electronic annotation of ER membrane localization from the UniProt subcellular-location vocabulary mapping. Matches the curated UniProt location and the experimental IDA evidence.
Reason: The IEA ER-membrane localization agrees with the UniProt subcellular location and with experimental evidence; correctly mapped.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
GO:0009101 glycoprotein biosynthetic process
IEA
GO_REF:0000002
KEEP AS NON CORE
Summary: InterPro2GO (IEA) mapping to glycoprotein biosynthesis. This is a broad downstream process term - DPM synthase supplies the Dol-P-Man donor for protein glycosylation, so DPM3 contributes indirectly, but glycoprotein biosynthesis is a general consequence rather than DPM3's direct/core role.
Reason: Correct in direction (DPM synthase output feeds glycoprotein biosynthesis) but broad and downstream; retained as a non-core process. The core BP is the biosynthesis of the Dol-P-Man donor itself.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Protein modification; protein glycosylation.
GO:0005515 protein binding
IPI
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
MARK AS OVER ANNOTATED
Summary: IPI protein-binding annotation capturing physical interaction of DPM3 with DPM1 (O60762), DPM2 (O94777), and Xenopus Dpm2 (Q9Z325). These are the functionally central interactions of DPM3, but the bare "protein binding" term is uninformative about the anchoring/adaptor role.
Reason: The DPM1/DPM2 interactions are real and central, but "protein binding" is an uninformative molecular-function term. The specific biology is better represented by the protein-membrane adaptor activity MF (GO:0043495) and the DPM synthase complex CC (GO:0033185), both already annotated.
Supporting Evidence:
PMID:10835346
via its C-terminal domain and with DPM2 via its N-terminal portion.
GO:0005515 protein binding
IPI
PMID:10944123
Initial enzyme for glycosylphosphatidylinositol biosynthesis...
MARK AS OVER ANNOTATED
Summary: IPI protein-binding annotation from the DPM2/GPI-GnT regulation study, recording physical interaction of DPM3 with DPM1 (O60762) and DPM2 (O94777) in the shared DPM-synthase/GPI-anchor context.
Reason: The interactions are genuine, but the bare "protein binding" term is uninformative; the anchoring role is captured by the protein-membrane adaptor MF and the DPM synthase complex CC terms.
Supporting Evidence:
PMID:10944123
DPM2, but not two other components of
GO:0005515 protein binding
IPI
PMID:23856421
Congenital disorder of glycosylation due to DPM1 mutations p...
MARK AS OVER ANNOTATED
Summary: IPI protein-binding annotation supported by the DPM1-CDG study, which showed the pathogenic DPM1 variant has reduced binding to DPM3, an essential non-catalytic subunit - i.e. it documents the DPM1-DPM3 physical interaction.
Reason: The DPM1-DPM3 interaction is real and disease-relevant, but "protein binding" is uninformative; the adaptor MF and complex CC terms convey the actual biology.
Supporting Evidence:
PMID:23856421
reduced binding to DPM3, an essential,
GO:0005789 endoplasmic reticulum membrane
NAS
PMID:9724629
DPM2 regulates biosynthesis of dolichol phosphate-mannose in...
ACCEPT
Summary: ComplexPortal NAS annotation of ER membrane localization. The cited study established that the DPM complex resides and functions in the ER membrane (where DPM2 makes a complex with DPM1 essential for ER localization of DPM1).
Reason: Consistent with all other localization evidence placing DPM3 and the DPM synthase complex in the ER membrane.
Supporting Evidence:
PMID:9724629
with DPM1 that is essential for the ER localization and stable expression of
GO:0033185 dolichol-phosphate-mannose synthase complex
IPI
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
ACCEPT
Summary: ComplexPortal IPI annotation of DPM3 as part of the DPM synthase complex, based on the physical demonstration that DPM3 is the third subunit associating with DPM1 and DPM2.
Reason: Directly supported experimental complex membership; this is a defining, core annotation for DPM3.
Supporting Evidence:
PMID:10835346
The third subunit, DPM3, comprises 92 amino acids associated with DPM1
GO:0043048 dolichyl monophosphate biosynthetic process
IDA
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
MODIFY
Summary: IDA annotation to dolichyl monophosphate (Dol-P) biosynthesis. This term denotes formation of dolichyl monophosphate, which is the SUBSTRATE of DPM synthase, not its product. DPM synthase (and thus DPM3) makes Dol-P-Man from Dol-P + GDP-mannose; it does not synthesize Dol-P itself. The evidence in PMID:10835346 concerns restoration of Dol-P-Man (DPM) biosynthesis.
Reason: The term is a misfit - DPM3 contributes to biosynthesis of dolichol phosphate mannose (Dol-P-Man), not dolichyl monophosphate. The IDA evidence supports the Dol-P-Man process term instead.
Supporting Evidence:
PMID:10835346
restored the biosynthesis of DPM with an
GO:0043495 protein-membrane adaptor activity
ISS
GO_REF:0000024
ACCEPT
Summary: ISS annotation (from ortholog Q4LDX8) to protein-membrane adaptor activity. This is the most informative molecular-function term for DPM3, whose role is to tether the catalytic DPM1 subunit (which lacks a transmembrane domain) to the ER membrane, bridging it to DPM2. This captures DPM3's true non-catalytic anchoring/scaffolding function.
Reason: Best represents DPM3's core molecular function - anchoring the soluble catalytic DPM1 to the ER membrane. Directly consistent with the UniProt FUNCTION statement and experimental data.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
GO:0180047 dolichol phosphate mannose biosynthetic process
IDA
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
ACCEPT
Summary: IDA annotation to dolichol phosphate mannose (Dol-P-Man) biosynthesis. This is the core biological process of DPM3, which is required for assembly and activity of the DPM synthase that produces Dol-P-Man. Overexpression of DPM3 in DPM2-null Lec15 cells restored DPM biosynthesis.
Reason: Correct core process, directly supported by experimental evidence that DPM3 is required for Dol-P-Man biosynthesis.
Supporting Evidence:
PMID:10835346
restored the biosynthesis of DPM with an
GO:0035269 protein O-linked glycosylation via mannose
ISS
GO_REF:0000024
KEEP AS NON CORE
Summary: ISS annotation to protein O-mannosylation. DPM synthase supplies the Dol-P-Man donor used for O-mannosylation of alpha-dystroglycan; loss of DPM3 causes an alpha-dystroglycanopathy with reduced O-mannosylation. However, this is a downstream process that consumes DPM synthase output rather than DPM3's own direct enzymatic step.
Reason: Biologically connected (and the basis of the DPM3-CDG dystroglycanopathy), but DPM3 acts upstream by producing the mannosyl donor; O-mannosylation itself is performed by other enzymes. Retained as non-core.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
reduced O-mannosylation of alpha-dystroglycan.
GO:0008047 enzyme activator activity
IDA
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
KEEP AS NON CORE
Summary: IDA annotation to enzyme activator activity. DPM3 increases DPM synthase output - overexpression restored DPM biosynthesis with an increase in DPM1, and DPM3 directly stabilizes DPM1. The activation, however, is achieved through stabilization/membrane anchoring of the catalytic subunit rather than classic allosteric enzyme activation.
Reason: Defensible - DPM3 raises catalytic activity of the complex - but the mechanism is structural stabilization/anchoring, which is more precisely captured by protein-membrane adaptor activity (GO:0043495). Retained as non-core rather than removed.
Supporting Evidence:
PMID:10835346
indicating that DPM3 directly stabilized DPM1.
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-4719354
ACCEPT
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway describing defective DPM3 failing to form Dol-P-Man. Consistent with all other ER-membrane evidence.
Reason: Reactome curated localization agrees with experimental and phylogenetic ER-membrane annotations.
Supporting Evidence:
Reactome:R-HSA-4719354
Normally, the DPM3 subunit tethers the catalytic DPM1 subunit to the ER membrane.
GO:0016020 membrane
HDA
PMID:19946888
Defining the membrane proteome of NK cells.
MARK AS OVER ANNOTATED
Summary: High-throughput MS detection of DPM3 in an NK-cell (YTS) membrane proteome, yielding a generic "membrane" localization. DPM3 is indeed a membrane protein, but this generic term is subsumed by the specific ER-membrane annotations.
Reason: Generic "membrane" is uninformative given the well-supported ER-membrane (GO:0005789) localization; derived from a large-scale membrane-proteome screen not specific to DPM3.
Supporting Evidence:
PMID:19946888
Isolated membranes were
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-162721
ACCEPT
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway for the Dol-P-Man synthesis reaction (dolichyl phosphate + GDP-mannose -> dolichyl phosphate D-mannose) catalysed by the ER-membrane DPM synthase.
Reason: Consistent with all other ER-membrane localization evidence.
Supporting Evidence:
Reactome:R-HSA-162721
a heterotrimeric protein embedded in the endoplasmic reticulum membrane
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-4717406
ACCEPT
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway describing defective DPM1 failing to form Dol-P-Man; the DPM complex (including DPM3) is annotated at the ER membrane.
Reason: Consistent with the other ER-membrane localization annotations.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-4719375
ACCEPT
Summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway describing defective DPM2 failing to form Dol-P-Man; the DPM complex (including DPM3) is annotated at the ER membrane.
Reason: Consistent with the other ER-membrane localization annotations.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
GO:0005783 endoplasmic reticulum
IDA
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
ACCEPT
Summary: IDA localization of DPM3 to the endoplasmic reticulum. This is the parent organelle term; the more specific and equally well-supported ER membrane term is the informative localization.
Reason: Correct localization, directly determined; retained (as the parent of the more specific ER-membrane term) but non-core relative to ER membrane.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass
GO:0033185 dolichol-phosphate-mannose synthase complex
IDA
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
ACCEPT
Summary: IDA annotation (UniProt) of DPM3 as part of the DPM synthase complex, based on the direct experimental demonstration that human DPM synthase consists of DPM1, DPM2 and DPM3.
Reason: Directly supported experimental complex membership; a defining core annotation.
Supporting Evidence:
PMID:10835346
The third subunit, DPM3, comprises 92 amino acids associated with DPM1
GO:0005789 endoplasmic reticulum membrane
IDA
PMID:10835346
Human dolichol-phosphate-mannose synthase consists of three ...
ACCEPT
Summary: IDA localization of DPM3 to the ER membrane, directly determined in the study that characterized the human DPM synthase complex.
Reason: Directly determined ER-membrane localization; the core, informative cellular-component annotation for DPM3.
Supporting Evidence:
file:human/DPM3/DPM3-uniprot.txt
Endoplasmic reticulum membrane; Multi-pass

Core Functions

DPM3 is the membrane-anchoring/adaptor subunit that tethers the catalytic DPM1 subunit (which has no transmembrane domain) to the endoplasmic reticulum membrane and bridges it to DPM2, as part of the dolichol-phosphate mannose (DPM) synthase complex.

Supporting Evidence:
  • file:human/DPM3/DPM3-uniprot.txt
    synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
  • PMID:10835346
    via its C-terminal domain and with DPM2 via its N-terminal portion.

References

Gene Ontology annotation through association of InterPro records with GO terms
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Human dolichol-phosphate-mannose synthase consists of three subunits, DPM1, DPM2 and DPM3.
  • DPM3 is a 92-amino-acid third subunit of the human DPM synthase complex that associates with DPM1 via its C-terminal domain and with DPM2 via its N-terminal portion; DPM3 directly stabilizes DPM1 and is required for DPM biosynthesis.
    "The third subunit, DPM3, comprises 92 amino acids associated with DPM1"
Initial enzyme for glycosylphosphatidylinositol biosynthesis requires PIG-P and is regulated by DPM2.
Defining the membrane proteome of NK cells.
Congenital disorder of glycosylation due to DPM1 mutations presenting with dystroglycanopathy-type congenital muscular dystrophy.
  • DPM3 is described as an essential, non-catalytic subunit of the DPM complex; a pathogenic DPM1 variant showed reduced binding to DPM3, indicating a disease mechanism via impaired DPM1-DPM3 interaction.
    "non-catalytic subunit of the DPM complex"
DPM2 regulates biosynthesis of dolichol phosphate-mannose in mammalian cells: correct subcellular localization and stabilization of DPM1, and binding of dolichol phosphate.
Reactome:R-HSA-162721
dolichyl phosphate + GDP-alpha-D-mannose -> dolichyl phosphate D-mannose
Reactome:R-HSA-4717406
Defective DPM1 does not transfer mannose to DOLP to form DOLPman
Reactome:R-HSA-4719354
Defective DPM3 does not transfer mannose to DOLP to form DOLPman
Reactome:R-HSA-4719375
Defective DPM2 does not transfer mannose to DOLP to form DOLPman
file:human/DPM3/DPM3-uniprot.txt
UniProtKB entry Q9P2X0 (DPM3_HUMAN)
  • DPM3 is the stabilizer subunit of the DPM synthase complex that tethers the catalytic DPM1 subunit to the ER membrane; it is a multi-pass ER membrane protein and its loss causes DPM3-CDG dystroglycanopathy.
    "synthase complex; tethers catalytic subunit DPM1 to the endoplasmic"

📚 Additional Documentation

Notes

(DPM3-notes.md)

DPM3 (Q9P2X0) review notes

Human DPM3 = dolichol-phosphate mannosyltransferase subunit 3 (anchoring subunit).
92 aa; two predicted TM helices (aa 8-28, 37-57). Belongs to the DPM3 family.
Deep research: falcon is OUT OF CREDITS (HTTP 402); no -deep-research-falcon.md was
generated. Review grounded in UniProt (Q9P2X0), the seeded GOA, and cached publications.

Core biology

DPM3 is the membrane-anchoring / stabilizer subunit of the heterotrimeric
dolichol-phosphate mannose (Dol-P-Man / DPM) synthase complex (DPM1/DPM2/DPM3). It is
non-catalytic — its function is structural/anchoring, not enzymatic.

  • The catalytic subunit DPM1 lacks a transmembrane domain; DPM3 tethers DPM1 to the ER
    membrane. [file:human/DPM3/DPM3-uniprot.txt "Stabilizer subunit of the dolichol-phosphate
    mannose (DPM)"; "synthase complex; tethers catalytic subunit DPM1 to the endoplasmic";
    "reticulum. {ECO:0000269|PubMed:10835346}."]
  • Within the complex, DPM3 associates with DPM1 via its C-terminal domain and with DPM2 via
    its N-terminal portion. [PMID:10835346 "The third subunit, DPM3, comprises 92 amino acids
    associated with DPM1"; "via its C-terminal domain and with DPM2 via its N-terminal portion."]
    [file:human/DPM3/DPM3-uniprot.txt "complex composed of DPM1, DPM2 and DPM3; within the
    complex, associates"; "with DPM1 via its C-terminal domain and with DPM2 via its N-terminal"]
  • Stability chain: DPM2 stabilizes DPM3; DPM3 stabilizes/directly stabilizes DPM1.
    Overexpression of DPM3 in Lec15 (DPM2-null) cells restored DPM biosynthesis with an increase
    in DPM1, i.e. DPM3 directly stabilizes DPM1. [PMID:10835346 "overexpression of DPM3 in";
    "restored the biosynthesis of DPM with an"; "indicating that DPM3 directly stabilized DPM1."]
  • The DPM synthase makes dolichol-phosphate-mannose (Dol-P-Man / DOLPman), the mannosyl donor
    used for GPI-anchor biosynthesis, N-glycan precursor assembly, and protein O- and
    C-mannosylation. [PMID:10835346 "Dolichol-phosphate-mannose (DPM) synthase generates mannosyl
    donors for"; "N-glycan and protein O- and C-mannosylation."]
  • UniProt pathway: Protein modification; protein glycosylation.
    [file:human/DPM3/DPM3-uniprot.txt "Protein modification; protein glycosylation."]

Localization

ER membrane, multi-pass membrane protein. [file:human/DPM3/DPM3-uniprot.txt "Endoplasmic
reticulum membrane; Multi-pass"] IDA localization to ER / ER membrane from PMID:10835346.
Reactome (TAS) also places the reaction and complex in the ER membrane. The HDA "membrane"
(GO:0016020) call comes from a large-scale NK-cell membrane-proteome MS study
(PMID:19946888), a generic membrane term subsumed by the ER-membrane annotations.

Disease

DPM3-CDG (congenital disorder of glycosylation type Io) — an
alpha-dystroglycanopathy-type muscular dystrophy. UniProt records two OMIM disease entries:
- MDDGC15 (limb-girdle, MIM:612937): muscle weakness, increased serum CK, dystrophic muscle
biopsy, reduced O-mannosylation of alpha-dystroglycan. [file:human/DPM3/DPM3-uniprot.txt
"MDDGC15 patients have muscle"; "weakness, increased serum creatine kinase, dystrophic
changes on muscle"; "reduced O-mannosylation of alpha-dystroglycan."]
- MDDGB15 (congenital with impaired intellectual development, MIM:618992).
The L85S variant reduces DPM1 binding and DPM synthase activity (Lefeber et al. 2009,
PMID:19576565, characterized in UniProt VARIANT feature). DPM1-CDG patients also show reduced
DPM1-DPM3 binding as the pathogenic mechanism. [PMID:23856421 "reduced binding to DPM3, an
essential,"; "non-catalytic subunit of the DPM complex"]

GOA annotation assessment (summary)

  • Core MF: GO:0043495 protein-membrane adaptor activity (ISS) — best captures the
    anchoring/tethering role; ACCEPT as core.
  • GO:0008047 enzyme activator activity (IDA, PMID:10835346) — DPM3 raises DPM synthase output
    by stabilizing DPM1; defensible but the effect is via stabilization/anchoring rather than
    classic allosteric activation. KEEP as non-core (the adaptor term is more informative).
  • GO:0005515 protein binding (IPI x4) — DPM1/DPM2 interactions. Uninformative bare term;
    MARK_AS_OVER_ANNOTATED (the specific adaptor MF + complex CC capture the biology).
  • CC: GO:0005789 ER membrane (multiple: IBA/IEA/NAS/TAS/IDA) — ACCEPT; GO:0005783 ER (IDA)
    ACCEPT (parent, non-core); GO:0016020 membrane (HDA) MARK_AS_OVER_ANNOTATED (generic);
    GO:0033185 DPM synthase complex (IBA/IPI/IDA) — ACCEPT as core complex.
  • BP: GO:0180047 dolichol phosphate mannose biosynthetic process (IDA) core; GO:0006488
    dolichol-linked oligosaccharide biosynthetic process (IBA) ACCEPT; GO:0043048 dolichyl
    monophosphate biosynthetic process (IDA) — this term is about making dolichyl monophosphate
    (Dol-P), NOT Dol-P-Man; DPM makes Dol-P-Man from Dol-P, so this looks like a mislabeled/too
    literal mapping — MODIFY to GO:0180047. GO:0009101 glycoprotein biosynthetic process (IEA)
    KEEP_AS_NON_CORE (downstream). GO:0035269 protein O-linked glycosylation via mannose (ISS)
    KEEP_AS_NON_CORE (downstream consumer of Dol-P-Man; not DPM3's direct activity).

📄 View Raw YAML

id: Q9P2X0
gene_symbol: DPM3
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: DPM3 is the small (92-residue) membrane-anchoring and stabilizer subunit
  of the heterotrimeric dolichol-phosphate mannose (Dol-P-Man / DPM) synthase complex,
  which also comprises the catalytic subunit DPM1 and the regulatory subunit DPM2.
  DPM synthase transfers mannose from cytosolic GDP-mannose to dolichyl phosphate at
  the endoplasmic reticulum membrane to produce dolichol-phosphate-mannose (Dol-P-Man),
  the essential lumenal mannosyl donor for GPI-anchor biosynthesis, N-glycan precursor
  assembly, and protein O- and C-mannosylation. DPM3 is non-catalytic; because the
  catalytic DPM1 subunit lacks a transmembrane domain, DPM3 (a multi-pass ER membrane
  protein) tethers DPM1 to the ER membrane and bridges the complex, associating with
  DPM1 through its C-terminal region and with DPM2 through its N-terminal region. This
  scaffolding stabilizes DPM1 and is required for assembly and activity of the DPM
  synthase. Loss of DPM3 function causes DPM3-CDG, an alpha-dystroglycanopathy-type
  congenital muscular dystrophy (with elevated serum creatine kinase, reduced
  O-mannosylation of alpha-dystroglycan, and cardiomyopathy in some patients).
alternative_products:
- name: 1 (Short)
  id: Q9P2X0-1
- name: 2 (Long)
  id: Q9P2X0-2
  sequence_note: VSP_001308
existing_annotations:
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Phylogenetic (IBA) localization of DPM3 to the ER membrane, where the
      DPM synthase complex acts. This is consistent with the experimentally determined
      localization and with DPM3 being a multi-pass ER membrane protein.
    action: ACCEPT
    reason: The ER membrane is the established site of the DPM synthase complex and
      of DPM3, corroborated by IDA localization and the UniProt subcellular location.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
    id: GO:0006488
    label: dolichol-linked oligosaccharide biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Phylogenetic (IBA) involvement in dolichol-linked oligosaccharide biosynthesis.
      DPM synthase produces Dol-P-Man, the mannosyl donor consumed during assembly
      of the dolichol-linked oligosaccharide (N-glycan precursor), so DPM3 contributes
      to this process as part of the complex.
    action: ACCEPT
    reason: DPM3 is required for DPM synthase activity, which supplies the Dol-P-Man
      mannosyl donor used in dolichol-linked oligosaccharide (LLO) assembly and
      downstream glycosylation.
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: N-glycan and protein O- and C-mannosylation.
- term:
    id: GO:0033185
    label: dolichol-phosphate-mannose synthase complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: part_of
  review:
    summary: Phylogenetic (IBA) assignment of DPM3 as part of the dolichol-phosphate-mannose
      synthase complex. This is the defining complex membership of DPM3 and is
      strongly supported experimentally.
    action: ACCEPT
    reason: DPM3 is one of the three subunits (DPM1/DPM2/DPM3) of the human DPM
      synthase complex; complex membership is directly established experimentally.
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: The third subunit, DPM3, comprises 92 amino acids associated
        with DPM1
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Electronic annotation of ER membrane localization from the UniProt
      subcellular-location vocabulary mapping. Matches the curated UniProt location
      and the experimental IDA evidence.
    action: ACCEPT
    reason: The IEA ER-membrane localization agrees with the UniProt subcellular
      location and with experimental evidence; correctly mapped.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
    id: GO:0009101
    label: glycoprotein biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: InterPro2GO (IEA) mapping to glycoprotein biosynthesis. This is a broad
      downstream process term - DPM synthase supplies the Dol-P-Man donor for protein
      glycosylation, so DPM3 contributes indirectly, but glycoprotein biosynthesis
      is a general consequence rather than DPM3's direct/core role.
    action: KEEP_AS_NON_CORE
    reason: Correct in direction (DPM synthase output feeds glycoprotein biosynthesis)
      but broad and downstream; retained as a non-core process. The core BP is the
      biosynthesis of the Dol-P-Man donor itself.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: 'Protein modification; protein glycosylation.'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10835346
  qualifier: enables
  review:
    summary: IPI protein-binding annotation capturing physical interaction of DPM3
      with DPM1 (O60762), DPM2 (O94777), and Xenopus Dpm2 (Q9Z325). These are the
      functionally central interactions of DPM3, but the bare "protein binding" term
      is uninformative about the anchoring/adaptor role.
    action: MARK_AS_OVER_ANNOTATED
    reason: The DPM1/DPM2 interactions are real and central, but "protein binding"
      is an uninformative molecular-function term. The specific biology is better
      represented by the protein-membrane adaptor activity MF (GO:0043495) and the
      DPM synthase complex CC (GO:0033185), both already annotated.
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: via its C-terminal domain and with DPM2 via its N-terminal
        portion.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10944123
  qualifier: enables
  review:
    summary: IPI protein-binding annotation from the DPM2/GPI-GnT regulation study,
      recording physical interaction of DPM3 with DPM1 (O60762) and DPM2 (O94777)
      in the shared DPM-synthase/GPI-anchor context.
    action: MARK_AS_OVER_ANNOTATED
    reason: The interactions are genuine, but the bare "protein binding" term is
      uninformative; the anchoring role is captured by the protein-membrane adaptor
      MF and the DPM synthase complex CC terms.
    supported_by:
    - reference_id: PMID:10944123
      supporting_text: DPM2, but not two other components of
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:23856421
  qualifier: enables
  review:
    summary: IPI protein-binding annotation supported by the DPM1-CDG study, which
      showed the pathogenic DPM1 variant has reduced binding to DPM3, an essential
      non-catalytic subunit - i.e. it documents the DPM1-DPM3 physical interaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: The DPM1-DPM3 interaction is real and disease-relevant, but "protein
      binding" is uninformative; the adaptor MF and complex CC terms convey the
      actual biology.
    supported_by:
    - reference_id: PMID:23856421
      supporting_text: reduced binding to DPM3, an essential,
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: NAS
  original_reference_id: PMID:9724629
  qualifier: located_in
  review:
    summary: ComplexPortal NAS annotation of ER membrane localization. The cited
      study established that the DPM complex resides and functions in the ER membrane
      (where DPM2 makes a complex with DPM1 essential for ER localization of DPM1).
    action: ACCEPT
    reason: Consistent with all other localization evidence placing DPM3 and the DPM
      synthase complex in the ER membrane.
    supported_by:
    - reference_id: PMID:9724629
      supporting_text: with DPM1 that is essential for the ER localization and stable
        expression of
- term:
    id: GO:0033185
    label: dolichol-phosphate-mannose synthase complex
  evidence_type: IPI
  original_reference_id: PMID:10835346
  qualifier: part_of
  review:
    summary: ComplexPortal IPI annotation of DPM3 as part of the DPM synthase complex,
      based on the physical demonstration that DPM3 is the third subunit associating
      with DPM1 and DPM2.
    action: ACCEPT
    reason: Directly supported experimental complex membership; this is a defining,
      core annotation for DPM3.
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: The third subunit, DPM3, comprises 92 amino acids associated
        with DPM1
- term:
    id: GO:0043048
    label: dolichyl monophosphate biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:10835346
  qualifier: involved_in
  review:
    summary: IDA annotation to dolichyl monophosphate (Dol-P) biosynthesis. This term
      denotes formation of dolichyl monophosphate, which is the SUBSTRATE of DPM
      synthase, not its product. DPM synthase (and thus DPM3) makes Dol-P-Man from
      Dol-P + GDP-mannose; it does not synthesize Dol-P itself. The evidence in
      PMID:10835346 concerns restoration of Dol-P-Man (DPM) biosynthesis.
    action: MODIFY
    reason: The term is a misfit - DPM3 contributes to biosynthesis of dolichol
      phosphate mannose (Dol-P-Man), not dolichyl monophosphate. The IDA evidence
      supports the Dol-P-Man process term instead.
    proposed_replacement_terms:
    - id: GO:0180047
      label: dolichol phosphate mannose biosynthetic process
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: restored the biosynthesis of DPM with an
- term:
    id: GO:0043495
    label: protein-membrane adaptor activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: ISS annotation (from ortholog Q4LDX8) to protein-membrane adaptor
      activity. This is the most informative molecular-function term for DPM3, whose
      role is to tether the catalytic DPM1 subunit (which lacks a transmembrane
      domain) to the ER membrane, bridging it to DPM2. This captures DPM3's true
      non-catalytic anchoring/scaffolding function.
    action: ACCEPT
    reason: Best represents DPM3's core molecular function - anchoring the soluble
      catalytic DPM1 to the ER membrane. Directly consistent with the UniProt FUNCTION
      statement and experimental data.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
- term:
    id: GO:0180047
    label: dolichol phosphate mannose biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:10835346
  qualifier: involved_in
  review:
    summary: IDA annotation to dolichol phosphate mannose (Dol-P-Man) biosynthesis.
      This is the core biological process of DPM3, which is required for assembly and
      activity of the DPM synthase that produces Dol-P-Man. Overexpression of DPM3
      in DPM2-null Lec15 cells restored DPM biosynthesis.
    action: ACCEPT
    reason: Correct core process, directly supported by experimental evidence that
      DPM3 is required for Dol-P-Man biosynthesis.
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: restored the biosynthesis of DPM with an
- term:
    id: GO:0035269
    label: protein O-linked glycosylation via mannose
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: ISS annotation to protein O-mannosylation. DPM synthase supplies the
      Dol-P-Man donor used for O-mannosylation of alpha-dystroglycan; loss of DPM3
      causes an alpha-dystroglycanopathy with reduced O-mannosylation. However, this
      is a downstream process that consumes DPM synthase output rather than DPM3's
      own direct enzymatic step.
    action: KEEP_AS_NON_CORE
    reason: Biologically connected (and the basis of the DPM3-CDG dystroglycanopathy),
      but DPM3 acts upstream by producing the mannosyl donor; O-mannosylation itself
      is performed by other enzymes. Retained as non-core.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: reduced O-mannosylation of alpha-dystroglycan.
- term:
    id: GO:0008047
    label: enzyme activator activity
  evidence_type: IDA
  original_reference_id: PMID:10835346
  qualifier: enables
  review:
    summary: IDA annotation to enzyme activator activity. DPM3 increases DPM synthase
      output - overexpression restored DPM biosynthesis with an increase in DPM1,
      and DPM3 directly stabilizes DPM1. The activation, however, is achieved through
      stabilization/membrane anchoring of the catalytic subunit rather than classic
      allosteric enzyme activation.
    action: KEEP_AS_NON_CORE
    reason: Defensible - DPM3 raises catalytic activity of the complex - but the
      mechanism is structural stabilization/anchoring, which is more precisely
      captured by protein-membrane adaptor activity (GO:0043495). Retained as
      non-core rather than removed.
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: indicating that DPM3 directly stabilized DPM1.
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-4719354
  qualifier: located_in
  review:
    summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
      describing defective DPM3 failing to form Dol-P-Man. Consistent with all other
      ER-membrane evidence.
    action: ACCEPT
    reason: Reactome curated localization agrees with experimental and phylogenetic
      ER-membrane annotations.
    supported_by:
    - reference_id: Reactome:R-HSA-4719354
      supporting_text: Normally, the DPM3 subunit tethers the catalytic DPM1 subunit
        to the ER membrane.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:19946888
  qualifier: located_in
  review:
    summary: High-throughput MS detection of DPM3 in an NK-cell (YTS) membrane
      proteome, yielding a generic "membrane" localization. DPM3 is indeed a
      membrane protein, but this generic term is subsumed by the specific ER-membrane
      annotations.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic "membrane" is uninformative given the well-supported ER-membrane
      (GO:0005789) localization; derived from a large-scale membrane-proteome screen
      not specific to DPM3.
    supported_by:
    - reference_id: PMID:19946888
      supporting_text: Isolated membranes were
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-162721
  qualifier: located_in
  review:
    summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
      for the Dol-P-Man synthesis reaction (dolichyl phosphate + GDP-mannose ->
      dolichyl phosphate D-mannose) catalysed by the ER-membrane DPM synthase.
    action: ACCEPT
    reason: Consistent with all other ER-membrane localization evidence.
    supported_by:
    - reference_id: Reactome:R-HSA-162721
      supporting_text: a heterotrimeric protein embedded in the endoplasmic reticulum
        membrane
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-4717406
  qualifier: located_in
  review:
    summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
      describing defective DPM1 failing to form Dol-P-Man; the DPM complex (including
      DPM3) is annotated at the ER membrane.
    action: ACCEPT
    reason: Consistent with the other ER-membrane localization annotations.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-4719375
  qualifier: located_in
  review:
    summary: Reactome TAS localization of DPM3 to the ER membrane, from the pathway
      describing defective DPM2 failing to form Dol-P-Man; the DPM complex (including
      DPM3) is annotated at the ER membrane.
    action: ACCEPT
    reason: Consistent with the other ER-membrane localization annotations.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:10835346
  qualifier: located_in
  review:
    summary: IDA localization of DPM3 to the endoplasmic reticulum. This is the
      parent organelle term; the more specific and equally well-supported ER membrane
      term is the informative localization.
    action: ACCEPT
    reason: Correct localization, directly determined; retained (as the parent of
      the more specific ER-membrane term) but non-core relative to ER membrane.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
- term:
    id: GO:0033185
    label: dolichol-phosphate-mannose synthase complex
  evidence_type: IDA
  original_reference_id: PMID:10835346
  qualifier: part_of
  review:
    summary: IDA annotation (UniProt) of DPM3 as part of the DPM synthase complex,
      based on the direct experimental demonstration that human DPM synthase consists
      of DPM1, DPM2 and DPM3.
    action: ACCEPT
    reason: Directly supported experimental complex membership; a defining core
      annotation.
    supported_by:
    - reference_id: PMID:10835346
      supporting_text: The third subunit, DPM3, comprises 92 amino acids associated
        with DPM1
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IDA
  original_reference_id: PMID:10835346
  qualifier: located_in
  review:
    summary: IDA localization of DPM3 to the ER membrane, directly determined in the
      study that characterized the human DPM synthase complex.
    action: ACCEPT
    reason: Directly determined ER-membrane localization; the core, informative
      cellular-component annotation for DPM3.
    supported_by:
    - reference_id: file:human/DPM3/DPM3-uniprot.txt
      supporting_text: 'Endoplasmic reticulum membrane; Multi-pass'
core_functions:
- description: DPM3 is the membrane-anchoring/adaptor subunit that tethers the
    catalytic DPM1 subunit (which has no transmembrane domain) to the endoplasmic
    reticulum membrane and bridges it to DPM2, as part of the dolichol-phosphate
    mannose (DPM) synthase complex.
  molecular_function:
    id: GO:0043495
    label: protein-membrane adaptor activity
  locations:
  - id: GO:0005789
    label: endoplasmic reticulum membrane
  in_complex:
    id: GO:0033185
    label: dolichol-phosphate-mannose synthase complex
  directly_involved_in:
  - id: GO:0180047
    label: dolichol phosphate mannose biosynthetic process
  supported_by:
  - reference_id: file:human/DPM3/DPM3-uniprot.txt
    supporting_text: synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
  - reference_id: PMID:10835346
    supporting_text: via its C-terminal domain and with DPM2 via its N-terminal portion.
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: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: PMID:10835346
  title: Human dolichol-phosphate-mannose synthase consists of three subunits, DPM1,
    DPM2 and DPM3.
  findings:
  - statement: DPM3 is a 92-amino-acid third subunit of the human DPM synthase complex
      that associates with DPM1 via its C-terminal domain and with DPM2 via its
      N-terminal portion; DPM3 directly stabilizes DPM1 and is required for DPM
      biosynthesis.
    supporting_text: The third subunit, DPM3, comprises 92 amino acids associated
      with DPM1
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Primary paper defining the three-subunit human DPM synthase and
      DPM3's anchoring/stabilizing role; abstract-only cache but directly supports
      all core claims.
- id: PMID:10944123
  title: Initial enzyme for glycosylphosphatidylinositol biosynthesis requires PIG-P
    and is regulated by DPM2.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Focuses on GPI-GnT and DPM2 regulation; used by IntAct as a
      protein-interaction source for DPM3. Supporting/corroborating for DPM3's
      interaction context.
- id: PMID:19946888
  title: Defining the membrane proteome of NK cells.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Large-scale NK-cell membrane-proteome MS study; source of the
      generic HDA "membrane" localization, not specific to DPM3.
- id: PMID:23856421
  title: Congenital disorder of glycosylation due to DPM1 mutations presenting with
    dystroglycanopathy-type congenital muscular dystrophy.
  findings:
  - statement: DPM3 is described as an essential, non-catalytic subunit of the DPM
      complex; a pathogenic DPM1 variant showed reduced binding to DPM3, indicating
      a disease mechanism via impaired DPM1-DPM3 interaction.
    supporting_text: non-catalytic subunit of the DPM complex
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: DPM1-CDG study; explicitly characterizes DPM3 as an essential
      non-catalytic subunit and documents the DPM1-DPM3 interaction relevant to
      disease.
- id: PMID:9724629
  title: 'DPM2 regulates biosynthesis of dolichol phosphate-mannose in mammalian cells:
    correct subcellular localization and stabilization of DPM1, and binding of dolichol
    phosphate.'
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Establishes the ER-membrane DPM synthase and DPM2-dependent
      stabilization/ER-localization of DPM1; ComplexPortal NAS source for DPM3
      ER-membrane localization.
- id: Reactome:R-HSA-162721
  title: dolichyl phosphate + GDP-alpha-D-mannose -> dolichyl phosphate D-mannose
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Reactome reaction for Dol-P-Man synthesis by the ER-membrane DPM
      synthase; source of a TAS ER-membrane localization for DPM3.
- id: Reactome:R-HSA-4717406
  title: Defective DPM1 does not transfer mannose to DOLP to form DOLPman
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Reactome disease reaction (defective DPM1); source of a TAS
      ER-membrane localization for DPM3.
- id: Reactome:R-HSA-4719354
  title: Defective DPM3 does not transfer mannose to DOLP to form DOLPman
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Reactome disease reaction (defective DPM3); states DPM3 tethers the
      catalytic DPM1 subunit to the ER membrane and links DPM3 loss to DPM3-CDG.
- id: Reactome:R-HSA-4719375
  title: Defective DPM2 does not transfer mannose to DOLP to form DOLPman
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Reactome disease reaction (defective DPM2); source of a TAS
      ER-membrane localization for DPM3.
- id: file:human/DPM3/DPM3-uniprot.txt
  title: UniProtKB entry Q9P2X0 (DPM3_HUMAN)
  findings:
  - statement: DPM3 is the stabilizer subunit of the DPM synthase complex that
      tethers the catalytic DPM1 subunit to the ER membrane; it is a multi-pass ER
      membrane protein and its loss causes DPM3-CDG dystroglycanopathy.
    supporting_text: synthase complex; tethers catalytic subunit DPM1 to the endoplasmic
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Curated UniProt record; source of FUNCTION, SUBUNIT, subcellular
      location, and disease statements used in this review.