ALG3

UniProt ID: Q92685
Organism: Homo sapiens
Review Status: INITIALIZED
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Gene Description

Dol-P-Man:Man(5)GlcNAc(2)-PP-dolichol alpha-1,3-mannosyltransferase (EC 2.4.1.258) that catalyzes the first endoplasmic reticulum (ER) lumenal step of dolichol-linked oligosaccharide (LLO) assembly for protein N-linked glycosylation. LLO assembly begins on the cytosolic face of the ER membrane and completes in the lumen; after Man5GlcNAc2-PP-dolichol is flipped to the lumenal face, ALG3 transfers the sixth mannose - the first mannose donated by dolichyl-phosphate-mannose (Dol-P-Man) rather than GDP-mannose - in an alpha-1,3 linkage to yield Man6GlcNAc2-PP-dolichol, the substrate for the next enzyme ALG9. It is a multi-pass ER membrane protein of the glycosyltransferase ALG3 family (CAZy GT58) acting on the lumenal side of the ER membrane. Deficiency causes ALG3-CDG (congenital disorder of glycosylation type Id, CDG1D).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005783 endoplasmic reticulum
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: Phylogenetic (IBA) localization of ALG3 to the endoplasmic reticulum. This is correct but is a broad parent of the more precise endoplasmic reticulum membrane (GO:0005789) where the enzyme actually resides as a multi-pass membrane protein.
Reason: Correct compartment but less specific than the experimentally supported ER membrane localization; retained as a broader, non-core supporting annotation.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0009101 glycoprotein biosynthetic process
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: Phylogenetic (IBA) involvement in glycoprotein biosynthesis. Correct in essence - ALG3 builds the LLO precursor used for N-glycosylation - but this is a broad parent of the more specific protein N-linked glycosylation (GO:0006487) and dolichol-linked oligosaccharide biosynthetic process (GO:0006488).
Reason: True but general; the specific BP terms (GO:0006487, GO:0006488) better capture the function and are separately annotated. Kept as non-core broader context.
Supporting Evidence:
PMID:10581255
the molecular defect in the index patient is a missense mutation in the gene encoding the mannosyltransferase that transfers mannose from dolichyl-phosphate mannose on to the lipid-linked oligosaccharide (LLO) intermediate
GO:0052925 dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: Phylogenetic (IBA) assignment of the specific catalytic activity - the Dol-P-Man-dependent alpha-1,3-mannosyltransferase (EC 2.4.1.258) that adds the sixth mannose to Man5GlcNAc2-PP-dolichol. This is the precise, correct molecular function and is directly supported experimentally.
Reason: Specific, experimentally validated core molecular function, concordant across IBA, EC/RHEA IEA, and human IDA evidence.
Supporting Evidence:
PMID:10581255
the mannosyltransferase that transfers mannose from dolichyl-phosphate mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
GO:0000030 mannosyltransferase activity
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro-based (IEA) generic mannosyltransferase activity. Correct at a broad level but far less specific than the experimentally established GO:0052925 (dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity).
Reason: The generic parent term under-annotates a well-characterized enzyme; replace with the specific EC 2.4.1.258 activity term.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
EC=2.4.1.258
GO:0005789 endoplasmic reticulum membrane
IEA
GO_REF:0000044 		ACCEPT
Summary: UniProt subcellular-location (IEA) mapping to the ER membrane, consistent with the experimental IDA localization and with the protein being a multi-pass ER membrane protein.
Reason: Correct core localization; agrees with experimental evidence and UniProt annotation.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0006487 protein N-linked glycosylation
IEA
GO_REF:0000117 		ACCEPT
Summary: ARBA machine-learning (IEA) involvement in protein N-linked glycosylation. Correct - ALG3 builds the LLO precursor employed in N-glycosylation - and duplicated by an experimental IDA annotation on the same term.
Reason: Accurate core biological process; concordant with the human IDA annotation.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
the glycan precursors employed in
GO:0052925 dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: RHEA/EC-based (IEA, EC 2.4.1.258, RHEA:29527) assignment of the specific Dol-P-Man-dependent alpha-1,3-mannosyltransferase activity. Matches the reaction described in UniProt and the experimental IDA.
Reason: Correct specific catalytic activity, supported by the curated EC/RHEA reaction and human experimental evidence.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
EC=2.4.1.258
GO:0005515 protein binding
IPI
PMID:21516116
Next-generation sequencing to generate interactome datasets. 		MARK AS OVER ANNOTATED
Summary: Protein-binding IPI from a high-throughput next-generation-sequencing interactome dataset (CREB3, O43889). The bare "protein binding" term is uninformative about molecular function and derives from a large-scale screen rather than a mechanistic study.
Reason: Bare protein binding from a high-throughput interactome screen conveys no specific molecular function; over-annotated per curation guidelines (not removed, as the interaction datum itself is real).
Supporting Evidence:
PMID:21516116
Next-generation sequencing to generate interactome datasets.
GO:0005515 protein binding
IPI
PMID:25910212
Widespread macromolecular interaction perturbations in human... 		MARK AS OVER ANNOTATED
Summary: Protein-binding IPI from a systematic study of interaction perturbations in human genetic disorders (CREB3 isoform, O43889-2). "Protein binding" is uninformative and derived from a high-throughput map.
Reason: Uninformative bare protein-binding term from a large-scale interactome perturbation study; over-annotated per guidelines.
Supporting Evidence:
PMID:25910212
Widespread macromolecular interaction perturbations in human genetic disorders.
GO:0005515 protein binding
IPI
PMID:29547901
Molecular partners of hNOT/ALG3, the human counterpart of th... 		MARK AS OVER ANNOTATED
Summary: Protein-binding IPIs (multiple partners including CREB3, OSBP, OSBPL9, LRP1, SYPL1) from a dedicated yeast two-hybrid study of hNOT/ALG3. Although this is an ALG3-focused study, the GO term captured is the uninformative generic "protein binding"; the interactions are suggestive of roles beyond glycosylation but do not define a specific molecular function for ALG3.
Reason: Even from a targeted interactome study, bare protein binding is uninformative as a molecular function; the interactions (e.g. CREB3, OSBPs) are retained context but not a core function. Not removed.
Supporting Evidence:
PMID:29547901
we identify 17 molecular partners of hNOT-1/ALG3-1
PMID:29547901
its in vivo interaction with the functionally linked proteins OSBP, OSBPL9 and LRP1, the SYPL1 protein and the transcription factor CREB3
GO:0005515 protein binding
IPI
PMID:31515488
Extensive disruption of protein interactions by genetic vari... 		MARK AS OVER ANNOTATED
Summary: Protein-binding IPI from a large-scale study of interaction disruption by genetic variants across the allele-frequency spectrum (CREB3, O43889). Bare protein binding from a high-throughput assay.
Reason: Uninformative generic protein-binding term from a high-throughput variant-interaction screen; over-annotated per guidelines.
Supporting Evidence:
PMID:31515488
Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
GO:0005515 protein binding
IPI
PMID:32296183
A reference map of the human binary protein interactome. 		MARK AS OVER ANNOTATED
Summary: Protein-binding IPIs from a systematic human binary interactome map (HuRI; partners ARL13B, CD79A, TMEM52B, SERP1, etc.). Bare "protein binding" from a genome-scale Y2H reference map.
Reason: Uninformative generic protein-binding term from a genome-scale binary interactome map; over-annotated per guidelines.
Supporting Evidence:
PMID:32296183
A reference map of the human binary protein interactome.
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
TAS
Reactome:R-HSA-446193 		ACCEPT
Summary: Reactome TAS placing ALG3 in dolichol-linked oligosaccharide (LLO) biosynthesis, the core pathway in which ALG3 adds the sixth mannose. Matches the experimental IDA on the same term.
Reason: Correct core biological process; concordant with human IDA evidence and the UniProt pathway annotation.
Supporting Evidence:
PMID:10581255
the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
GO:0098553 lumenal side of endoplasmic reticulum membrane
IC
PMID:10581255
Carbohydrate deficient glycoprotein syndrome type IV: defici... 		ACCEPT
Summary: Curator inference (IC) that ALG3 acts on the lumenal side of the ER membrane, consistent with the established topology of LLO assembly in which the reaction ALG3 catalyzes occurs after the Man5GlcNAc2-PP-dolichol intermediate is flipped into the ER lumen.
Reason: Correct and precise topological localization matching the known lumenal step of LLO assembly catalyzed by ALG3.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
The assembly of dolichol-linked
file:human/ALG3/ALG3-uniprot.txt
In the lumen of the endoplasmic reticulum,
GO:0005789 endoplasmic reticulum membrane
IDA
PMID:10581255
Carbohydrate deficient glycoprotein syndrome type IV: defici... 		ACCEPT
Summary: Experimental (IDA) localization of ALG3 to the ER membrane, where the multi-pass membrane enzyme catalyzes the lumenal mannosyltransfer step of LLO assembly.
Reason: Experimentally supported core localization; consistent with UniProt (multi-pass ER membrane protein) and the enzyme's role in ER LLO biosynthesis.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0006487 protein N-linked glycosylation
IDA
PMID:10581255
Carbohydrate deficient glycoprotein syndrome type IV: defici... 		ACCEPT
Summary: Experimental (IDA) involvement in protein N-linked glycosylation - ALG3 deficiency causes abnormal N-glycosylation due to transfer of truncated oligosaccharides, establishing its role in the pathway.
Reason: Directly supported core biological process; ALG3 defect impairs N-glycosylation.
Supporting Evidence:
PMID:10581255
N-glycosylation is abnormal because of the transfer of truncated oligosaccharides
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
IDA
PMID:10581255
Carbohydrate deficient glycoprotein syndrome type IV: defici... 		ACCEPT
Summary: Experimental (IDA) involvement in dolichol-linked oligosaccharide biosynthesis; ALG3 deficiency causes accumulation of the Man5GlcNAc2-PP-dolichol LLO intermediate, directly demonstrating its role in the pathway.
Reason: Directly supported core biological process; the enzyme adds the sixth mannose of the LLO and its loss stalls the pathway.
Supporting Evidence:
PMID:10581255
The defect results in the accumulation of the LLO intermediate
GO:0052925 dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
IDA
PMID:10581255
Carbohydrate deficient glycoprotein syndrome type IV: defici... 		ACCEPT
Summary: Experimental (IDA) demonstration of the specific Dol-P-Man-dependent alpha-1,3-mannosyltransferase activity (EC 2.4.1.258) transferring mannose from dolichyl-phosphate-mannose onto Man5GlcNAc2-PP-dolichol. This is the defining, experimentally validated core molecular function.
Reason: Primary experimental evidence for the core catalytic function; the CDG1D G118D variant abolishes this activity.
Supporting Evidence:
PMID:10581255
the mannosyltransferase that transfers mannose from dolichyl-phosphate mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
GO:0000033 alpha-1,3-mannosyltransferase activity
TAS
Reactome:R-HSA-446188 		MODIFY
Summary: Reactome TAS assigning alpha-1,3-mannosyltransferase activity. Correct linkage specificity but a broad parent of the precise, substrate-defined GO:0052925 (dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity, EC 2.4.1.258).
Reason: Correct but under-specified for a well-characterized enzyme; replace with the specific EC 2.4.1.258 activity term.
Supporting Evidence:
PMID:10581255
the mannosyltransferase that transfers mannose from dolichyl-phosphate mannose
GO:0000033 alpha-1,3-mannosyltransferase activity
TAS
Reactome:R-HSA-4720473 		MODIFY
Summary: Reactome TAS (from the defective-ALG3 CDG1D reaction) assigning alpha-1,3-mannosyltransferase activity. As above, correct but a broad parent of the substrate-specific GO:0052925.
Reason: Correct but under-specified; replace with the specific EC 2.4.1.258 activity term to match the well-characterized function.
Supporting Evidence:
PMID:10581255
the mannosyltransferase that transfers mannose from dolichyl-phosphate mannose
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-4720473 		ACCEPT
Summary: Reactome TAS localizing ALG3 to the ER membrane, concordant with the experimental IDA and UniProt subcellular-location annotations.
Reason: Correct core localization; agrees with experimental evidence.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-446188 		ACCEPT
Summary: Reactome TAS localizing ALG3 to the ER membrane (from the mannose-transfer reaction), concordant with the experimental IDA and UniProt annotations.
Reason: Correct core localization; agrees with experimental evidence.
Supporting Evidence:
file:human/ALG3/ALG3-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane

Core Functions

Dol-P-Man-dependent alpha-1,3-mannosyltransferase (EC 2.4.1.258) that catalyzes the first ER-lumenal step of dolichol-linked oligosaccharide assembly, transferring the sixth mannose from dolichyl-phosphate-mannose in an alpha-1,3 linkage onto Man5GlcNAc2-PP-dolichol to produce Man6GlcNAc2-PP-dolichol for protein N-linked glycosylation.

Molecular Function:
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
Directly Involved In:
dolichol-linked oligosaccharide biosynthetic process
Cellular Locations:
endoplasmic reticulum membrane
Supporting Evidence:
  • PMID:10581255
    the mannosyltransferase that transfers mannose from dolichyl-phosphate mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol

Participates in protein N-linked glycosylation by generating the lipid-linked oligosaccharide precursor; loss of activity (as in ALG3-CDG) causes accumulation of the Man5GlcNAc2-PP-dolichol intermediate and transfer of truncated oligosaccharides.

Molecular Function:
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
Directly Involved In:
protein N-linked glycosylation
Cellular Locations:
endoplasmic reticulum membrane
Supporting Evidence:
  • PMID:10581255
    N-glycosylation is abnormal because of the transfer of truncated oligosaccharides

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000033
Annotation inferences using phylogenetic trees
GO_REF:0000044
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
GO_REF:0000117
Electronic Gene Ontology annotations created by ARBA machine learning models
GO_REF:0000120
Combined Automated Annotation using Multiple IEA Methods
PMID:10581255
Carbohydrate deficient glycoprotein syndrome type IV: deficiency of dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase.
  • Identified ALG3 as the deficient enzyme in CDGS type IV (now ALG3-CDG/CDG1D); the mannosyltransferase transfers mannose from dolichyl-phosphate-mannose onto the Man5GlcNAc2-PP-dolichol LLO intermediate, and is the structural/functional orthologue of yeast ALG3.
    "the mannosyltransferase that transfers mannose from dolichyl-phosphate mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol"
PMID:21516116
Next-generation sequencing to generate interactome datasets.
PMID:25910212
Widespread macromolecular interaction perturbations in human genetic disorders.
PMID:29547901
Molecular partners of hNOT/ALG3, the human counterpart of the Drosophila NOT and yeast ALG3 gene, suggest its involvement in distinct cellular processes relevant to congenital disorders of glycosylation, cancer, neurodegeneration and a variety of further pathologies.
  • Yeast two-hybrid study identifying 17 molecular partners of hNOT/ALG3 including homodimers and in vivo interactions with OSBP, OSBPL9, LRP1, SYPL1 and the transcription factor CREB3.
    "we identify 17 molecular partners of hNOT-1/ALG3-1"
PMID:31515488
Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
PMID:32296183
A reference map of the human binary protein interactome.
Reactome:R-HSA-446188
ALG3 transfers Man to N-glycan precursor (GlcNAc)2 (Man)5 (PP-Dol)1
Reactome:R-HSA-446193
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
Reactome:R-HSA-4720473
Defective ALG3 does not add mannose to the N-glycan precursor
file:human/ALG3/ALG3-uniprot.txt
UniProt entry Q92685 (ALG3_HUMAN)

📚 Additional Documentation

Notes

(ALG3-notes.md)

ALG3 (Q92685) review notes

Summary of function

ALG3 is the human Dol-P-Man:Man(5)GlcNAc(2)-PP-dolichol alpha-1,3-mannosyltransferase
(EC 2.4.1.258), the enzyme catalysing the first ER-lumenal step of dolichol-linked
oligosaccharide (LLO) assembly for protein N-glycosylation.

  • Assembly of the LLO begins on the cytosolic face of the ER membrane and finishes
    in the lumen. After Man5GlcNAc2-PP-dolichol is flipped to the lumenal face, ALG3
    transfers the sixth mannose (the first mannose derived from dolichyl-phosphate-mannose,
    Dol-P-Man    , rather than GDP-Man) in an alpha-1,3 linkage onto Man5GlcNAc2-PP-Dol to
    give Man6GlcNAc2-PP-dolichol. The product is the substrate for ALG9, the next enzyme
    in the pathway [UniProt Q92685 FUNCTION; PMID:10581255].
  • ALG3 is a polytopic ER membrane protein (11 predicted TM helices; UniProt features),
    member of the glycosyltransferase ALG3 family / CAZy GT58, active on the lumenal side of
    the ER membrane.
  • It is the structural and functional orthologue of S. cerevisiae ALG3
    PMID:10581255.

Disease

Deficiency causes ALG3-CDG (congenital disorder of glycosylation type Id / CDG1D;
MIM:601110), originally described as CDGS type IV. Characterised by microcephaly,
severe epilepsy, minimal psychomotor development, dysmorphism, and partial deficiency of
sialic acids in serum glycoproteins; the defect causes accumulation of the
Man5GlcNAc2-PP-Dol intermediate and transfer of truncated oligosaccharides
[PMID:10581255; PMID:15840742]. Pathogenic variants include G118D and R171Q.

Key references

  • PMID:10581255 (Körner et al. 1999, EMBO J): identified ALG3 as the deficient
    mannosyltransferase in CDGS type IV; defines catalytic activity, pathway, subcellular
    location, and disease. Abstract-only in cache (full_text_available: false) but abstract
    is rich. This is the primary experimental reference for MF/BP/CC IDA/IC annotations.
  • PMID:15840742 (Sun et al. 2005): CDG1D variant R171Q; clinical presentation.
  • PMID:29547901 (Hacker et al. 2018, Hum Mol Genet): Y2H interactome of hNOT/ALG3;
    homodimers, and interactions with OSBP, OSBPL9, LRP1, SYPL1, CREB3. Abstract-only.
    Provides functional context for the IntAct protein-binding annotations. 33% identity
    with yeast ALG3.

Annotation review decisions

GOA MF term = GO:0052925 (dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase
activity) — this is the specific, correct current MF; used in IBA, IEA(EC/RHEA), and IDA.

  • Core MF: GO:0052925 (IDA PMID:10581255, plus IBA and EC/RHEA IEA) — ACCEPT.
  • GO:0000030 mannosyltransferase activity (IEA InterPro) and GO:0000033
    alpha-1,3-mannosyltransferase activity (TAS Reactome): correct but less specific
    parents of GO:0052925 -> MODIFY to GO:0052925 (over-general MF).
  • Core BP: GO:0006488 dolichol-linked oligosaccharide biosynthetic process (IDA + TAS) and
    GO:0006487 protein N-linked glycosylation (IDA + IEA) — ACCEPT.
  • GO:0009101 glycoprotein biosynthetic process (IBA): correct but broad parent of
    GO:0006487 -> KEEP_AS_NON_CORE (acceptable broader IBA).
  • Core CC: GO:0005789 endoplasmic reticulum membrane (IDA + IEA + TAS) — ACCEPT;
    GO:0098553 lumenal side of ER membrane (IC) — ACCEPT (precise topology).
    GO:0005783 endoplasmic reticulum (IBA) — KEEP_AS_NON_CORE (broader parent of ER membrane).
  • GO:0005515 protein binding (IPI x11 across 5 interactome papers): bare, uninformative
    MF from high-throughput screens -> MARK_AS_OVER_ANNOTATED (per policy, not REMOVE).

📄 View Raw YAML

 
id: Q92685
gene_symbol: ALG3
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: Dol-P-Man:Man(5)GlcNAc(2)-PP-dolichol alpha-1,3-mannosyltransferase (EC
  2.4.1.258) that catalyzes the first endoplasmic reticulum (ER) lumenal step of dolichol-linked
  oligosaccharide (LLO) assembly for protein N-linked glycosylation. LLO assembly begins
  on the cytosolic face of the ER membrane and completes in the lumen; after Man5GlcNAc2-PP-dolichol
  is flipped to the lumenal face, ALG3 transfers the sixth mannose - the first mannose
  donated by dolichyl-phosphate-mannose (Dol-P-Man) rather than GDP-mannose - in an alpha-1,3
  linkage to yield Man6GlcNAc2-PP-dolichol, the substrate for the next enzyme ALG9. It
  is a multi-pass ER membrane protein of the glycosyltransferase ALG3 family (CAZy GT58)
  acting on the lumenal side of the ER membrane. Deficiency causes ALG3-CDG (congenital
  disorder of glycosylation type Id, CDG1D).
alternative_products:
- name: '1'
  id: Q92685-1
- name: '2'
  id: Q92685-2
  sequence_note: VSP_042738
existing_annotations:
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Phylogenetic (IBA) localization of ALG3 to the endoplasmic reticulum. This
      is correct but is a broad parent of the more precise endoplasmic reticulum membrane
      (GO:0005789) where the enzyme actually resides as a multi-pass membrane protein.
    action: KEEP_AS_NON_CORE
    reason: Correct compartment but less specific than the experimentally supported ER
      membrane localization; retained as a broader, non-core supporting annotation.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Endoplasmic reticulum membrane"
- term:
    id: GO:0009101
    label: glycoprotein biosynthetic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Phylogenetic (IBA) involvement in glycoprotein biosynthesis. Correct in
      essence - ALG3 builds the LLO precursor used for N-glycosylation - but this is a
      broad parent of the more specific protein N-linked glycosylation (GO:0006487) and
      dolichol-linked oligosaccharide biosynthetic process (GO:0006488).
    action: KEEP_AS_NON_CORE
    reason: True but general; the specific BP terms (GO:0006487, GO:0006488) better capture
      the function and are separately annotated. Kept as non-core broader context.
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: the molecular defect in the index patient is a missense mutation
        in the gene encoding the mannosyltransferase that transfers mannose from dolichyl-phosphate
        mannose on to the lipid-linked oligosaccharide (LLO) intermediate
- term:
    id: GO:0052925
    label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: Phylogenetic (IBA) assignment of the specific catalytic activity - the Dol-P-Man-dependent
      alpha-1,3-mannosyltransferase (EC 2.4.1.258) that adds the sixth mannose to Man5GlcNAc2-PP-dolichol.
      This is the precise, correct molecular function and is directly supported experimentally.
    action: ACCEPT
    reason: Specific, experimentally validated core molecular function, concordant across
      IBA, EC/RHEA IEA, and human IDA evidence.
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: the mannosyltransferase that transfers mannose from dolichyl-phosphate
        mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
- term:
    id: GO:0000030
    label: mannosyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: InterPro-based (IEA) generic mannosyltransferase activity. Correct at a broad
      level but far less specific than the experimentally established GO:0052925 (dol-P-Man:Man(5)GlcNAc(2)-PP-Dol
      alpha-1,3-mannosyltransferase activity).
    action: MODIFY
    reason: The generic parent term under-annotates a well-characterized enzyme; replace
      with the specific EC 2.4.1.258 activity term.
    proposed_replacement_terms:
    - id: GO:0052925
      label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: EC=2.4.1.258
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: UniProt subcellular-location (IEA) mapping to the ER membrane, consistent
      with the experimental IDA localization and with the protein being a multi-pass ER
      membrane protein.
    action: ACCEPT
    reason: Correct core localization; agrees with experimental evidence and UniProt annotation.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Endoplasmic reticulum membrane"
- term:
    id: GO:0006487
    label: protein N-linked glycosylation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: ARBA machine-learning (IEA) involvement in protein N-linked glycosylation.
      Correct - ALG3 builds the LLO precursor employed in N-glycosylation - and duplicated
      by an experimental IDA annotation on the same term.
    action: ACCEPT
    reason: Accurate core biological process; concordant with the human IDA annotation.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: the glycan precursors employed in
- term:
    id: GO:0052925
    label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: RHEA/EC-based (IEA, EC 2.4.1.258, RHEA:29527) assignment of the specific
      Dol-P-Man-dependent alpha-1,3-mannosyltransferase activity. Matches the reaction
      described in UniProt and the experimental IDA.
    action: ACCEPT
    reason: Correct specific catalytic activity, supported by the curated EC/RHEA reaction
      and human experimental evidence.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: EC=2.4.1.258
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21516116
  qualifier: enables
  review:
    summary: Protein-binding IPI from a high-throughput next-generation-sequencing interactome
      dataset (CREB3, O43889). The bare "protein binding" term is uninformative about
      molecular function and derives from a large-scale screen rather than a mechanistic
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: Bare protein binding from a high-throughput interactome screen conveys no specific
      molecular function; over-annotated per curation guidelines (not removed, as the
      interaction datum itself is real).
    supported_by:
    - reference_id: PMID:21516116
      supporting_text: Next-generation sequencing to generate interactome datasets.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25910212
  qualifier: enables
  review:
    summary: Protein-binding IPI from a systematic study of interaction perturbations in
      human genetic disorders (CREB3 isoform, O43889-2). "Protein binding" is uninformative
      and derived from a high-throughput map.
    action: MARK_AS_OVER_ANNOTATED
    reason: Uninformative bare protein-binding term from a large-scale interactome perturbation
      study; over-annotated per guidelines.
    supported_by:
    - reference_id: PMID:25910212
      supporting_text: Widespread macromolecular interaction perturbations in human genetic
        disorders.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:29547901
  qualifier: enables
  review:
    summary: Protein-binding IPIs (multiple partners including CREB3, OSBP, OSBPL9, LRP1,
      SYPL1) from a dedicated yeast two-hybrid study of hNOT/ALG3. Although this is an
      ALG3-focused study, the GO term captured is the uninformative generic "protein binding";
      the interactions are suggestive of roles beyond glycosylation but do not define a
      specific molecular function for ALG3.
    action: MARK_AS_OVER_ANNOTATED
    reason: Even from a targeted interactome study, bare protein binding is uninformative
      as a molecular function; the interactions (e.g. CREB3, OSBPs) are retained context
      but not a core function. Not removed.
    supported_by:
    - reference_id: PMID:29547901
      supporting_text: we identify 17 molecular partners of hNOT-1/ALG3-1
    - reference_id: PMID:29547901
      supporting_text: its in vivo interaction with the functionally linked proteins OSBP,
        OSBPL9 and LRP1, the SYPL1 protein and the transcription factor CREB3
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31515488
  qualifier: enables
  review:
    summary: Protein-binding IPI from a large-scale study of interaction disruption by
      genetic variants across the allele-frequency spectrum (CREB3, O43889). Bare protein
      binding from a high-throughput assay.
    action: MARK_AS_OVER_ANNOTATED
    reason: Uninformative generic protein-binding term from a high-throughput variant-interaction
      screen; over-annotated per guidelines.
    supported_by:
    - reference_id: PMID:31515488
      supporting_text: Extensive disruption of protein interactions by genetic variants
        across the allele frequency spectrum in human populations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: Protein-binding IPIs from a systematic human binary interactome map (HuRI;
      partners ARL13B, CD79A, TMEM52B, SERP1, etc.). Bare "protein binding" from a genome-scale
      Y2H reference map.
    action: MARK_AS_OVER_ANNOTATED
    reason: Uninformative generic protein-binding term from a genome-scale binary interactome
      map; over-annotated per guidelines.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: A reference map of the human binary protein interactome.
- term:
    id: GO:0006488
    label: dolichol-linked oligosaccharide biosynthetic process
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-446193
  qualifier: involved_in
  review:
    summary: Reactome TAS placing ALG3 in dolichol-linked oligosaccharide (LLO) biosynthesis,
      the core pathway in which ALG3 adds the sixth mannose. Matches the experimental IDA
      on the same term.
    action: ACCEPT
    reason: Correct core biological process; concordant with human IDA evidence and the
      UniProt pathway annotation.
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
- term:
    id: GO:0098553
    label: lumenal side of endoplasmic reticulum membrane
  evidence_type: IC
  original_reference_id: PMID:10581255
  qualifier: is_active_in
  review:
    summary: Curator inference (IC) that ALG3 acts on the lumenal side of the ER membrane,
      consistent with the established topology of LLO assembly in which the reaction ALG3
      catalyzes occurs after the Man5GlcNAc2-PP-dolichol intermediate is flipped into the
      ER lumen.
    action: ACCEPT
    reason: Correct and precise topological localization matching the known lumenal step
      of LLO assembly catalyzed by ALG3.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: The assembly of dolichol-linked
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: In the lumen of the endoplasmic reticulum,
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IDA
  original_reference_id: PMID:10581255
  qualifier: is_active_in
  review:
    summary: Experimental (IDA) localization of ALG3 to the ER membrane, where the multi-pass
      membrane enzyme catalyzes the lumenal mannosyltransfer step of LLO assembly.
    action: ACCEPT
    reason: Experimentally supported core localization; consistent with UniProt (multi-pass
      ER membrane protein) and the enzyme's role in ER LLO biosynthesis.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Endoplasmic reticulum membrane"
- term:
    id: GO:0006487
    label: protein N-linked glycosylation
  evidence_type: IDA
  original_reference_id: PMID:10581255
  qualifier: involved_in
  review:
    summary: Experimental (IDA) involvement in protein N-linked glycosylation - ALG3 deficiency
      causes abnormal N-glycosylation due to transfer of truncated oligosaccharides, establishing
      its role in the pathway.
    action: ACCEPT
    reason: Directly supported core biological process; ALG3 defect impairs N-glycosylation.
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: N-glycosylation is abnormal because of the transfer of truncated
        oligosaccharides
- term:
    id: GO:0006488
    label: dolichol-linked oligosaccharide biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:10581255
  qualifier: involved_in
  review:
    summary: Experimental (IDA) involvement in dolichol-linked oligosaccharide biosynthesis;
      ALG3 deficiency causes accumulation of the Man5GlcNAc2-PP-dolichol LLO intermediate,
      directly demonstrating its role in the pathway.
    action: ACCEPT
    reason: Directly supported core biological process; the enzyme adds the sixth mannose
      of the LLO and its loss stalls the pathway.
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: The defect results in the accumulation of the LLO intermediate
- term:
    id: GO:0052925
    label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
  evidence_type: IDA
  original_reference_id: PMID:10581255
  qualifier: enables
  review:
    summary: Experimental (IDA) demonstration of the specific Dol-P-Man-dependent alpha-1,3-mannosyltransferase
      activity (EC 2.4.1.258) transferring mannose from dolichyl-phosphate-mannose onto
      Man5GlcNAc2-PP-dolichol. This is the defining, experimentally validated core molecular
      function.
    action: ACCEPT
    reason: Primary experimental evidence for the core catalytic function; the CDG1D G118D
      variant abolishes this activity.
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: the mannosyltransferase that transfers mannose from dolichyl-phosphate
        mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
- term:
    id: GO:0000033
    label: alpha-1,3-mannosyltransferase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-446188
  qualifier: enables
  review:
    summary: Reactome TAS assigning alpha-1,3-mannosyltransferase activity. Correct linkage
      specificity but a broad parent of the precise, substrate-defined GO:0052925 (dol-P-Man:Man(5)GlcNAc(2)-PP-Dol
      alpha-1,3-mannosyltransferase activity, EC 2.4.1.258).
    action: MODIFY
    reason: Correct but under-specified for a well-characterized enzyme; replace with the
      specific EC 2.4.1.258 activity term.
    proposed_replacement_terms:
    - id: GO:0052925
      label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: the mannosyltransferase that transfers mannose from dolichyl-phosphate
        mannose
- term:
    id: GO:0000033
    label: alpha-1,3-mannosyltransferase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-4720473
  qualifier: enables
  review:
    summary: Reactome TAS (from the defective-ALG3 CDG1D reaction) assigning alpha-1,3-mannosyltransferase
      activity. As above, correct but a broad parent of the substrate-specific GO:0052925.
    action: MODIFY
    reason: Correct but under-specified; replace with the specific EC 2.4.1.258 activity
      term to match the well-characterized function.
    proposed_replacement_terms:
    - id: GO:0052925
      label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
    supported_by:
    - reference_id: PMID:10581255
      supporting_text: the mannosyltransferase that transfers mannose from dolichyl-phosphate
        mannose
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-4720473
  qualifier: located_in
  review:
    summary: Reactome TAS localizing ALG3 to the ER membrane, concordant with the experimental
      IDA and UniProt subcellular-location annotations.
    action: ACCEPT
    reason: Correct core localization; agrees with experimental evidence.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Endoplasmic reticulum membrane"
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-446188
  qualifier: located_in
  review:
    summary: Reactome TAS localizing ALG3 to the ER membrane (from the mannose-transfer
      reaction), concordant with the experimental IDA and UniProt annotations.
    action: ACCEPT
    reason: Correct core localization; agrees with experimental evidence.
    supported_by:
    - reference_id: file:human/ALG3/ALG3-uniprot.txt
      supporting_text: "SUBCELLULAR LOCATION: Endoplasmic reticulum membrane"
core_functions:
- description: Dol-P-Man-dependent alpha-1,3-mannosyltransferase (EC 2.4.1.258) that catalyzes
    the first ER-lumenal step of dolichol-linked oligosaccharide assembly, transferring
    the sixth mannose from dolichyl-phosphate-mannose in an alpha-1,3 linkage onto Man5GlcNAc2-PP-dolichol
    to produce Man6GlcNAc2-PP-dolichol for protein N-linked glycosylation.
  molecular_function:
    id: GO:0052925
    label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
  directly_involved_in:
  - id: GO:0006488
    label: dolichol-linked oligosaccharide biosynthetic process
  locations:
  - id: GO:0005789
    label: endoplasmic reticulum membrane
  supported_by:
  - reference_id: PMID:10581255
    supporting_text: the mannosyltransferase that transfers mannose from dolichyl-phosphate
      mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
- description: Participates in protein N-linked glycosylation by generating the lipid-linked
    oligosaccharide precursor; loss of activity (as in ALG3-CDG) causes accumulation of
    the Man5GlcNAc2-PP-dolichol intermediate and transfer of truncated oligosaccharides.
  molecular_function:
    id: GO:0052925
    label: dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity
  directly_involved_in:
  - id: GO:0006487
    label: protein N-linked glycosylation
  locations:
  - id: GO:0005789
    label: endoplasmic reticulum membrane
  supported_by:
  - reference_id: PMID:10581255
    supporting_text: N-glycosylation is abnormal because of the transfer of truncated
      oligosaccharides
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  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: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10581255
  title: 'Carbohydrate deficient glycoprotein syndrome type IV: deficiency of dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl
    mannosyltransferase.'
  findings:
  - statement: Identified ALG3 as the deficient enzyme in CDGS type IV (now ALG3-CDG/CDG1D);
      the mannosyltransferase transfers mannose from dolichyl-phosphate-mannose onto the
      Man5GlcNAc2-PP-dolichol LLO intermediate, and is the structural/functional orthologue
      of yeast ALG3.
    supporting_text: the mannosyltransferase that transfers mannose from dolichyl-phosphate
      mannose on to the lipid-linked oligosaccharide (LLO) intermediate Man(5)GlcNAc(2)-PP-dolichol
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PubMed-verified primary reference (Korner et al. 1999, EMBO J); establishes
      catalytic activity, pathway, ER localization and CDG1D. Cached entry is abstract-only
      (full_text_available false) but the abstract directly supports the MF/BP/CC annotations.
- id: PMID:21516116
  title: Next-generation sequencing to generate interactome datasets.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: High-throughput interactome methods paper; source of a bare protein-binding
      IPI (CREB3). Real interaction datum but uninformative as molecular function.
- id: PMID:25910212
  title: Widespread macromolecular interaction perturbations in human genetic disorders.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Large-scale interaction-perturbation study; source of a bare protein-binding
      IPI (CREB3 isoform). Not informative for ALG3 molecular function.
- id: PMID:29547901
  title: Molecular partners of hNOT/ALG3, the human counterpart of the Drosophila
    NOT and yeast ALG3 gene, suggest its involvement in distinct cellular processes
    relevant to congenital disorders of glycosylation, cancer, neurodegeneration and
    a variety of further pathologies.
  findings:
  - statement: Yeast two-hybrid study identifying 17 molecular partners of hNOT/ALG3
      including homodimers and in vivo interactions with OSBP, OSBPL9, LRP1, SYPL1 and
      the transcription factor CREB3.
    supporting_text: we identify 17 molecular partners of hNOT-1/ALG3-1
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: ALG3-focused Y2H interactome study; provides functional context for the
      IntAct protein-binding annotations. Abstract-only in cache. Interactions are suggestive
      but do not define a specific molecular function beyond the mannosyltransferase activity.
- id: PMID:31515488
  title: Extensive disruption of protein interactions by genetic variants across the
    allele frequency spectrum in human populations.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: High-throughput variant-interaction screen; source of a bare protein-binding
      IPI (CREB3). Uninformative for ALG3 molecular function.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Genome-scale binary interactome map (HuRI); source of several bare protein-binding
      IPIs. Uninformative for ALG3 molecular function.
- id: Reactome:R-HSA-446188
  title: ALG3 transfers Man to N-glycan precursor (GlcNAc)2 (Man)5 (PP-Dol)1
  findings: []
- id: Reactome:R-HSA-446193
  title: Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide,
    LLO) and transfer to a nascent protein
  findings: []
- id: Reactome:R-HSA-4720473
  title: Defective ALG3 does not add mannose to the N-glycan precursor
  findings: []
- id: file:human/ALG3/ALG3-uniprot.txt
  title: UniProt entry Q92685 (ALG3_HUMAN)
  findings: []