ALG12

UniProt ID: Q9BV10
Organism: Homo sapiens
Review Status: INITIALIZED
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Gene Description

ALG12 is an endoplasmic reticulum membrane, ER-lumen-facing dolichyl-phosphate-mannose (Dol-P-Man)-dependent alpha-1,6-mannosyltransferase (glycosyltransferase family GT22; EC 2.4.1.260) that acts in the biosynthesis of the dolichol-linked oligosaccharide (LLO) precursor used for protein asparagine (N)-linked glycosylation. In the ER lumen it adds the eighth mannose residue in an alpha-1,6 linkage from Dol-P-Man onto Man7GlcNAc2-PP-dolichol to produce Man8GlcNAc2-PP-dolichol. It is a multi-pass ER membrane protein. Loss of its mannosyltransferase activity causes ALG12-CDG (congenital disorder of glycosylation type Ig), a multisystem disease with under-glycosylated serum glycoproteins.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000009 alpha-1,6-mannosyltransferase activity
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) call of alpha-1,6-mannosyltransferase activity. This is correct for ALG12, which forms the alpha-1,6 linkage when adding the eighth mannose of LLO assembly, though it is a general parent of the specific Dol-P-Man-dependent term GO:0052917.
Reason: Correct molecular activity, consistent with the experimentally verified alpha-1,6-mannosyltransferase function. Retained as an accurate parent of the more specific core MF term GO:0052917.
Supporting Evidence:
PMID:12217961
we describe a deficiency in the ALG12 ER
file:human/ALG12/ALG12-uniprot.txt
adds the eighth mannose residue in an alpha-1,6 linkage onto
GO:0005789 endoplasmic reticulum membrane
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) localization of active ALG12 to the ER membrane. ALG12 is a multi-pass ER membrane protein whose catalytic site faces the ER lumen, consistent with the lumenal LLO mannose additions.
Reason: Correct subcellular location; the enzyme is an integral ER membrane protein acting on the lumenal LLO intermediate.
Supporting Evidence:
file:human/ALG12/ALG12-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0006487 protein N-linked glycosylation
IBA
GO_REF:0000033
ACCEPT
Summary: Phylogenetic (IBA) involvement in protein N-linked glycosylation. ALG12 builds the LLO precursor that is transferred en bloc to asparagine residues of nascent proteins, so it is genuinely part of the N-glycosylation process.
Reason: Core biological process. ALG12 contributes the eighth mannose of the dolichol-linked precursor used for protein N-glycosylation.
Supporting Evidence:
PMID:11983712
used for protein N-glycosylation
PMID:12217961
N-linked glycans are first
GO:0005789 endoplasmic reticulum membrane
IEA
GO_REF:0000044
ACCEPT
Summary: Electronic (UniProt SubCell mapping) location in the ER membrane. Agrees with the curated SUBCELLULAR LOCATION and the IBA/TAS ER-membrane calls.
Reason: Correct location, consistent with all other evidence for ER membrane localization.
Supporting Evidence:
file:human/ALG12/ALG12-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0016757 glycosyltransferase activity
IEA
GO_REF:0000002
ACCEPT
Summary: InterPro2GO (IEA) mapping from the GT22/Glyco_transf_22 domain to the broad parent term glycosyltransferase activity. Correct but uninformative relative to the specific mannosyltransferase terms.
Reason: Correct high-level activity inferred from the glycosyltransferase family 22 domain; acceptable as a broad IEA parent of the specific core MF term.
Supporting Evidence:
file:human/ALG12/ALG12-uniprot.txt
Belongs to the glycosyltransferase 22 family
GO:0052917 dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
IEA
GO_REF:0000120
ACCEPT
Summary: Electronic (RHEA/EC 2.4.1.260) mapping to the exact Dol-P-Man-dependent alpha-1,6-mannosyltransferase reaction. This is the precise catalytic activity of ALG12 and matches the experimentally supported EC.
Reason: Exactly correct molecular function; corroborated by the EXP and IMP annotations to the same term.
Supporting Evidence:
PMID:11983712
dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
file:human/ALG12/ALG12-uniprot.txt
EC=2.4.1.260
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
TAS
Reactome:R-HSA-446193
ACCEPT
Summary: Reactome (TAS) involvement in dolichol-linked oligosaccharide biosynthesis. ALG12 catalyzes one step (eighth mannose addition) of LLO assembly, so this is a correct and core biological process.
Reason: Core biological process, corroborated by the IMP and IDA annotations to the same term from CDG-Ig studies.
Supporting Evidence:
PMID:11983712
deficient in their capacity to add the eighth mannose residue onto the
GO:0052917 dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
EXP
PMID:12217961
ALG12 mannosyltransferase defect in congenital disorder of g...
ACCEPT
Summary: Experimental annotation of the specific Dol-P-Man-dependent alpha-1,6-mannosyltransferase activity. Patient fibroblasts show a defect in the ALG12 alpha-1,6-mannosyltransferase, with yeast alg12 complementation confirming the enzymatic identity of the human protein.
Reason: Directly experimentally supported core molecular function; the exact current GOA MF term for ALG12 (EC 2.4.1.260).
Supporting Evidence:
PMID:12217961
we describe a deficiency in the ALG12 ER
PMID:12217961
the dolichyl pyrophosphate-GlcNAc(2)Man(7)-dependent ALG12 alpha1,6
GO:0098553 lumenal side of endoplasmic reticulum membrane
IC
PMID:12217961
ALG12 mannosyltransferase defect in congenital disorder of g...
ACCEPT
Summary: Curator-inferred (IC) localization of active ALG12 to the lumenal side of the ER membrane. The lumenal mannose additions of LLO assembly (using Dol-P-Man) occur on the ER lumenal face, consistent with the ER alpha-1,6-mannosyltransferase described for ALG12.
Reason: Correct and more specific than the generic ER membrane term; reflects the lumenal topology of the catalytic activity.
Supporting Evidence:
PMID:12217961
we describe a deficiency in the ALG12 ER
file:human/ALG12/ALG12-uniprot.txt
In the lumen of the endoplasmic reticulum
GO:0006487 protein N-linked glycosylation
IMP
PMID:11983712
Congenital disorders of glycosylation type Ig is defined by ...
ACCEPT
Summary: Mutant-phenotype (IMP) evidence for involvement in protein N-linked glycosylation. CDG-Ig patient fibroblasts with defective ALG12 show under-glycosylated glycoproteins, and the phenotype is rescued by wild-type ALG12, tying ALG12 function to N-glycosylation.
Reason: Experimentally supported core biological process.
Supporting Evidence:
PMID:11983712
under-glycosylated serum glycoproteins
GO:0006487 protein N-linked glycosylation
IMP
PMID:12093361
Deficiency of dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl mannosy...
ACCEPT
Summary: Independent mutant-phenotype (IMP) evidence for involvement in protein N-linked glycosylation. A second CDG-Ig patient with reduced ALG12 mannosyltransferase activity shows partial loss of N-glycan side chains on serum transferrin, rescued by wild-type ALG12.
Reason: Experimentally supported core biological process, independently corroborating PMID:11983712.
Supporting Evidence:
PMID:12093361
the partial loss of complete N-glycan
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
IMP
PMID:11983712
Congenital disorders of glycosylation type Ig is defined by ...
ACCEPT
Summary: Mutant-phenotype (IMP) evidence for involvement in dolichol-linked oligosaccharide biosynthesis. Loss of ALG12 blocks addition of the eighth mannose onto the LLO precursor; wild-type gene transduction normalizes the phenotype.
Reason: Experimentally supported core biological process (the direct step ALG12 catalyzes in LLO assembly).
Supporting Evidence:
PMID:11983712
deficient in their capacity to add the eighth mannose residue onto the
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
IMP
PMID:12093361
Deficiency of dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl mannosy...
ACCEPT
Summary: Independent mutant-phenotype (IMP) evidence for involvement in dolichol-linked oligosaccharide biosynthesis. Reduced ALG12 activity causes accumulation of the Man7GlcNAc2-PP-Dol intermediate.
Reason: Experimentally supported core biological process, corroborating the other IMP/IDA annotations.
Supporting Evidence:
PMID:12093361
leading to the accumulation of Man(7)GlcNAc(2)-PP-Dol, which was transferred to
GO:0052917 dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
IMP
PMID:11983712
Congenital disorders of glycosylation type Ig is defined by ...
ACCEPT
Summary: Mutant-phenotype (IMP) evidence for the specific Dol-P-Man-dependent alpha-1,6-mannosyltransferase activity. The CDG-Ig patient's fibroblasts cannot add the eighth mannose, and the human ALG12 cDNA rescues the defect, identifying ALG12 as this enzyme.
Reason: Experimentally supported core molecular function; the exact current GOA MF term for ALG12.
Supporting Evidence:
PMID:11983712
dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
GO:0052917 dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
IMP
PMID:12093361
Deficiency of dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl mannosy...
ACCEPT
Summary: Independent mutant-phenotype (IMP) evidence for the Dol-P-Man-dependent mannosyltransferase activity. Patient fibroblasts show severely reduced Dol-P-Man:Man7GlcNAc2-PP-Dol mannosyltransferase activity, normalized by wild-type ALG12 expression.
Reason: Experimentally supported core molecular function, independently corroborating PMID:11983712.
Supporting Evidence:
PMID:12093361
Retroviral expression of the wild-type
GO:0000030 mannosyltransferase activity
TAS
Reactome:R-HSA-446198
MODIFY
Summary: Reactome (TAS) mannosyltransferase activity. Correct but overly general: the specific and experimentally supported activity is the Dol-P-Man-dependent alpha-1,6-mannosyltransferase GO:0052917.
Reason: Too general. ALG12's activity is captured precisely by GO:0052917; replace the generic mannosyltransferase term with the specific one.
Supporting Evidence:
PMID:11983712
dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
GO:0000030 mannosyltransferase activity
TAS
Reactome:R-HSA-4720497
MODIFY
Summary: Reactome (TAS) mannosyltransferase activity (from the defective-ALG12 disease reaction). Same over-general term as R-HSA-446198.
Reason: Too general; the specific activity term GO:0052917 should be used.
Supporting Evidence:
PMID:11983712
dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-4720497
ACCEPT
Summary: Reactome (TAS) location in the ER membrane. Consistent with all other ER-membrane evidence.
Reason: Correct subcellular location.
Supporting Evidence:
file:human/ALG12/ALG12-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0016020 membrane
HDA
PMID:19946888
Defining the membrane proteome of NK cells.
MARK AS OVER ANNOTATED
Summary: High-throughput proteomics (HDA) detection of ALG12 in a membrane fraction from an NK-like cell line. The generic "membrane" term adds no information beyond the specific ER membrane localization.
Reason: Uninformative generic membrane term from a large-scale membrane-proteome survey (1843 proteins); the specific, well-supported location is ER membrane. Not incorrect, but over-broad and non-core.
Supporting Evidence:
PMID:19946888
identified 1843 proteins with high confidence scores
GO:0006488 dolichol-linked oligosaccharide biosynthetic process
IDA
PMID:11983712
Congenital disorders of glycosylation type Ig is defined by ...
ACCEPT
Summary: Direct-assay (IDA) evidence that ALG12 acts within dolichol-linked oligosaccharide biosynthesis, with the acts_upstream_of_or_within qualifier. The eighth mannose addition step ALG12 catalyzes is directly demonstrated by the biochemical defect and its rescue.
Reason: Experimentally supported core biological process.
Supporting Evidence:
PMID:11983712
deficient in their capacity to add the eighth mannose residue onto the
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-446198
ACCEPT
Summary: Reactome (TAS) location in the ER membrane. Consistent with all other ER-membrane evidence.
Reason: Correct subcellular location.
Supporting Evidence:
file:human/ALG12/ALG12-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0005783 endoplasmic reticulum
NAS
PMID:12217961
ALG12 mannosyltransferase defect in congenital disorder of g...
ACCEPT
Summary: Non-traceable author statement (NAS) placing ALG12 in the endoplasmic reticulum. Broader than the ER membrane term but correct; ALG12 is an ER alpha-1,6-mannosyltransferase.
Reason: Correct but less specific than the ER membrane annotations; retained as an accurate broader location.
Supporting Evidence:
PMID:12217961
we describe a deficiency in the ALG12 ER
GO:0006457 protein folding
NAS
PMID:12217961
ALG12 mannosyltransferase defect in congenital disorder of g...
MARK AS OVER ANNOTATED
Summary: Non-traceable author statement (NAS) associating ALG12 with protein folding. ALG12 is a mannosyltransferase that builds the N-glycan precursor; N-glycosylation supports downstream glycoprotein folding/quality control, but ALG12 does not itself carry out protein folding. This mislabels the molecular role.
Reason: Over-annotation via a downstream/indirect consequence. ALG12's direct role is dolichol-linked oligosaccharide biosynthesis for N-glycosylation (GO:0006488, GO:0006487); "protein folding" is an indirect effect and does not describe ALG12's function. Non-core.
Supporting Evidence:
PMID:12217961
N-linked glycans are first

Core Functions

Dol-P-Man-dependent alpha-1,6-mannosyltransferase that adds the eighth mannose from dolichyl-phosphate-mannose in an alpha-1,6 linkage onto Man7GlcNAc2-PP-dolichol to produce Man8GlcNAc2-PP-dolichol in the ER lumen (EC 2.4.1.260).

Supporting Evidence:
  • PMID:11983712
    dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
  • PMID:11983712
    deficient in their capacity to add the eighth mannose residue onto the

ER membrane mannosyltransferase that contributes the eighth mannose of the dolichol-linked oligosaccharide precursor transferred en bloc to asparagine residues during protein N-linked glycosylation.

Supporting Evidence:

References

Gene Ontology annotation through association of InterPro records with GO terms
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
Combined Automated Annotation using Multiple IEA Methods
Congenital disorders of glycosylation type Ig is defined by a deficiency in dolichyl-P-mannose:Man7GlcNAc2-PP-dolichyl mannosyltransferase.
  • Human ALG12, the ortholog of yeast ALG12, encodes the dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl alpha6-mannosyltransferase; CDG-Ig patient fibroblasts are deficient in adding the eighth mannose onto the LLO precursor, and the defect (F142V) is rescued by wild-type ALG12.
    "deficient in their capacity to add the eighth mannose residue onto the"
Deficiency of dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl mannosyltransferase causes congenital disorder of glycosylation type Ig.
  • A second CDG-Ig patient shows severely reduced ER Dol-P-Man:Man7GlcNAc2-PP-Dol mannosyltransferase activity with accumulation of Man7GlcNAc2-PP-Dol and partial loss of N-glycan side chains; wild-type ALG12 normalizes activity.
    "leading to the accumulation of Man(7)GlcNAc(2)-PP-Dol, which was transferred to"
ALG12 mannosyltransferase defect in congenital disorder of glycosylation type lg.
  • Describes deficiency in the ALG12 ER alpha-1,6-mannosyltransferase; ER lumenal LLO context; yeast alg12 complementation confirms enzyme identity; defines CDG-Ig.
    "we describe a deficiency in the ALG12 ER"
Defining the membrane proteome of NK cells.
  • Large-scale membrane-proteome survey of an NK-like cell line detecting ALG12 among 1843 proteins; basis of the generic membrane annotation only.
    "identified 1843 proteins with high confidence scores"
Reactome:R-HSA-446193
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
Reactome:R-HSA-446198
ALG12 transfers Man to N-glycan precursor (GlcNAc)2 (Man)7 (PP-Dol)1
Reactome:R-HSA-4720497
Defective ALG12 does not add mannose to the N-glycan precursor
file:human/ALG12/ALG12-uniprot.txt
UniProtKB Q9BV10 (ALG12_HUMAN) curated entry
  • ALG12 is an ER membrane, multi-pass Dol-P-Man-dependent alpha-1,6-mannosyltransferase (EC 2.4.1.260) of the glycosyltransferase 22 family that adds the eighth mannose onto Man7GlcNAc2-PP-dolichol in the ER lumen; defects cause CDG type Ig.
    "adds the eighth mannose residue in an alpha-1,6 linkage onto"

📚 Additional Documentation

Notes

(ALG12-notes.md)

ALG12 (human, Q9BV10) review notes

Summary of function

ALG12 is an ER membrane, ER-lumenal-facing alpha-1,6-mannosyltransferase (glycosyltransferase
family GT22; CAZy GT22, Pfam PF03901 Glyco_transf_22) of the dolichol-linked oligosaccharide
(LLO) assembly pathway for protein N-glycosylation. It transfers the eighth mannose from
dolichyl-phosphate-mannose (Dol-P-Man) in an alpha-1,6 linkage onto Man7GlcNAc2-PP-dolichol
to give Man8GlcNAc2-PP-dolichol (EC 2.4.1.260; RHEA:29535). The lumenal mannose additions of LLO
assembly use Dol-P-Man as donor, not GDP-Man.

  • [UniProt Q9BV10 FUNCTION, "In the lumen of the endoplasmic reticulum, adds the eighth mannose residue in an alpha-1,6 linkage onto Man(7)GlcNAc(2)-PP-dolichol to produce Man(8)GlcNAc(2)-PP-dolichol."]
  • [UniProt Q9BV10 SUBCELLULAR LOCATION "Endoplasmic reticulum membrane"; "Multi-pass membrane protein" — 12 predicted TM helices]
  • [UniProt Q9BV10 SIMILARITY "Belongs to the glycosyltransferase 22 family."]

Disease

Loss of ALG12 mannosyltransferase activity causes ALG12-CDG / congenital disorder of
glycosylation type Ig (CDG-Ig, MIM:607143)
, a multisystem disorder with under-glycosylated
serum glycoproteins, psychomotor/developmental retardation, hypotonia, dysmorphism,
immunodeficiency.

Key references (all abstract-only in cache; quotes verbatim from abstracts)

  • PMID:11983712 (Chantret et al 2002, J Biol Chem) — identified human ALG12 as ortholog of
    yeast ALG12 encoding the dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl alpha6-mannosyltransferase;
    CDG-Ig patient fibroblasts "deficient in their capacity to add the eighth mannose residue onto
    the lipid-linked oligosaccharide precursor"; homozygous F142V; WT rescue. Establishes MF, BP,
    and disease. Basis of the EXP/IMP/IDA annotations.
  • PMID:12093361 (Thiel et al 2002, Biochem J) — "Deficiency of the endoplasmic reticulum
    enzyme dolichyl-phosphate mannose (Dol-P-Man):Man(7)GlcNAc(2)-PP-dolichyl mannosyltransferase";
    reduced activity, Man7GlcNAc2-PP-Dol accumulation; L158P + C-terminal truncation; WT rescue.
  • PMID:12217961 (Grubenmann et al 2002, Hum Mol Genet) — "a deficiency in the ALG12 ER
    alpha1,6-mannosyltransferase"; ER/lumenal localization inference; yeast alg12 complementation;
    T67M and R146Q. Basis of the IC (lumenal side of ER membrane) and NAS (ER; protein folding)
    annotations.
  • PMID:19946888 (Ghosh et al 2010, J Mass Spectrom) — NK-cell membrane proteome MS study
    (1843 proteins); basis of HDA "membrane" annotation. Generic membrane localization only.

Annotation decisions (high level)

  • Core MF: GO:0052917 (dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity) —
    EXP/IMP ACCEPT (core). Exact GOA current term (EC 2.4.1.260).
  • GO:0000009 (alpha-1,6-mannosyltransferase activity, IBA) ACCEPT — correct but less specific
    than GO:0052917.
  • GO:0000030 (mannosyltransferase activity, TAS Reactome x2) MODIFY -> GO:0052917 (too general).
  • GO:0016757 (glycosyltransferase activity, IEA InterPro) ACCEPT as correct-but-broad parent.
  • Core BP: GO:0006488 (dolichol-linked oligosaccharide biosynthetic process) IMP/IDA/TAS and
    GO:0006487 (protein N-linked glycosylation) IBA/IMP — ACCEPT (core).
  • Core CC: GO:0005789 (ER membrane) IBA/IEA/TAS — ACCEPT. GO:0098553 (lumenal side of ER
    membrane, IC) ACCEPT (more specific, correct topology). GO:0005783 (ER, NAS) ACCEPT as broader.
  • GO:0016020 (membrane, HDA PMID:19946888) MARK_AS_OVER_ANNOTATED — uninformative generic
    membrane from a proteome survey; ER membrane is the specific term.
  • GO:0006457 (protein folding, NAS PMID:12217961) — MARK_AS_OVER_ANNOTATED. ALG12 does not fold
    proteins; N-glycosylation is upstream of/supports folding but "protein folding" mis-describes
    the molecular role. Downstream/indirect.

📄 View Raw YAML

id: Q9BV10
gene_symbol: ALG12
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  ALG12 is an endoplasmic reticulum membrane, ER-lumen-facing
  dolichyl-phosphate-mannose (Dol-P-Man)-dependent alpha-1,6-mannosyltransferase
  (glycosyltransferase family GT22; EC 2.4.1.260) that acts in the biosynthesis
  of the dolichol-linked oligosaccharide (LLO) precursor used for protein
  asparagine (N)-linked glycosylation. In the ER lumen it adds the eighth
  mannose residue in an alpha-1,6 linkage from Dol-P-Man onto
  Man7GlcNAc2-PP-dolichol to produce Man8GlcNAc2-PP-dolichol. It is a
  multi-pass ER membrane protein. Loss of its mannosyltransferase activity
  causes ALG12-CDG (congenital disorder of glycosylation type Ig), a
  multisystem disease with under-glycosylated serum glycoproteins.
existing_annotations:
- term:
    id: GO:0000009
    label: alpha-1,6-mannosyltransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Phylogenetic (IBA) call of alpha-1,6-mannosyltransferase activity. This is
      correct for ALG12, which forms the alpha-1,6 linkage when adding the eighth
      mannose of LLO assembly, though it is a general parent of the specific
      Dol-P-Man-dependent term GO:0052917.
    action: ACCEPT
    reason: >-
      Correct molecular activity, consistent with the experimentally verified
      alpha-1,6-mannosyltransferase function. Retained as an accurate parent of
      the more specific core MF term GO:0052917.
    supported_by:
    - reference_id: PMID:12217961
      supporting_text: >-
        we describe a deficiency in the ALG12 ER
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        adds the eighth mannose residue in an alpha-1,6 linkage onto
- 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 active ALG12 to the ER membrane. ALG12
      is a multi-pass ER membrane protein whose catalytic site faces the ER
      lumen, consistent with the lumenal LLO mannose additions.
    action: ACCEPT
    reason: >-
      Correct subcellular location; the enzyme is an integral ER membrane protein
      acting on the lumenal LLO intermediate.
    supported_by:
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
- term:
    id: GO:0006487
    label: protein N-linked glycosylation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      Phylogenetic (IBA) involvement in protein N-linked glycosylation. ALG12
      builds the LLO precursor that is transferred en bloc to asparagine
      residues of nascent proteins, so it is genuinely part of the
      N-glycosylation process.
    action: ACCEPT
    reason: >-
      Core biological process. ALG12 contributes the eighth mannose of the
      dolichol-linked precursor used for protein N-glycosylation.
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        used for protein N-glycosylation
    - reference_id: PMID:12217961
      supporting_text: >-
        N-linked glycans are first
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      Electronic (UniProt SubCell mapping) location in the ER membrane. Agrees
      with the curated SUBCELLULAR LOCATION and the IBA/TAS ER-membrane calls.
    action: ACCEPT
    reason: >-
      Correct location, consistent with all other evidence for ER membrane
      localization.
    supported_by:
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
- term:
    id: GO:0016757
    label: glycosyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      InterPro2GO (IEA) mapping from the GT22/Glyco_transf_22 domain to the broad
      parent term glycosyltransferase activity. Correct but uninformative
      relative to the specific mannosyltransferase terms.
    action: ACCEPT
    reason: >-
      Correct high-level activity inferred from the glycosyltransferase family 22
      domain; acceptable as a broad IEA parent of the specific core MF term.
    supported_by:
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        Belongs to the glycosyltransferase 22 family
- term:
    id: GO:0052917
    label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: >-
      Electronic (RHEA/EC 2.4.1.260) mapping to the exact Dol-P-Man-dependent
      alpha-1,6-mannosyltransferase reaction. This is the precise catalytic
      activity of ALG12 and matches the experimentally supported EC.
    action: ACCEPT
    reason: >-
      Exactly correct molecular function; corroborated by the EXP and IMP
      annotations to the same term.
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        EC=2.4.1.260
- 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) involvement in dolichol-linked oligosaccharide biosynthesis.
      ALG12 catalyzes one step (eighth mannose addition) of LLO assembly, so this
      is a correct and core biological process.
    action: ACCEPT
    reason: >-
      Core biological process, corroborated by the IMP and IDA annotations to the
      same term from CDG-Ig studies.
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        deficient in their capacity to add the eighth mannose residue onto the
- term:
    id: GO:0052917
    label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
  evidence_type: EXP
  original_reference_id: PMID:12217961
  qualifier: enables
  review:
    summary: >-
      Experimental annotation of the specific Dol-P-Man-dependent
      alpha-1,6-mannosyltransferase activity. Patient fibroblasts show a defect in
      the ALG12 alpha-1,6-mannosyltransferase, with yeast alg12 complementation
      confirming the enzymatic identity of the human protein.
    action: ACCEPT
    reason: >-
      Directly experimentally supported core molecular function; the exact current
      GOA MF term for ALG12 (EC 2.4.1.260).
    supported_by:
    - reference_id: PMID:12217961
      supporting_text: >-
        we describe a deficiency in the ALG12 ER
    - reference_id: PMID:12217961
      supporting_text: >-
        the dolichyl pyrophosphate-GlcNAc(2)Man(7)-dependent ALG12 alpha1,6
- term:
    id: GO:0098553
    label: lumenal side of endoplasmic reticulum membrane
  evidence_type: IC
  original_reference_id: PMID:12217961
  qualifier: is_active_in
  review:
    summary: >-
      Curator-inferred (IC) localization of active ALG12 to the lumenal side of
      the ER membrane. The lumenal mannose additions of LLO assembly (using
      Dol-P-Man) occur on the ER lumenal face, consistent with the ER
      alpha-1,6-mannosyltransferase described for ALG12.
    action: ACCEPT
    reason: >-
      Correct and more specific than the generic ER membrane term; reflects the
      lumenal topology of the catalytic activity.
    supported_by:
    - reference_id: PMID:12217961
      supporting_text: >-
        we describe a deficiency in the ALG12 ER
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        In the lumen of the endoplasmic reticulum
- term:
    id: GO:0006487
    label: protein N-linked glycosylation
  evidence_type: IMP
  original_reference_id: PMID:11983712
  qualifier: involved_in
  review:
    summary: >-
      Mutant-phenotype (IMP) evidence for involvement in protein N-linked
      glycosylation. CDG-Ig patient fibroblasts with defective ALG12 show
      under-glycosylated glycoproteins, and the phenotype is rescued by wild-type
      ALG12, tying ALG12 function to N-glycosylation.
    action: ACCEPT
    reason: >-
      Experimentally supported core biological process.
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        under-glycosylated serum glycoproteins
- term:
    id: GO:0006487
    label: protein N-linked glycosylation
  evidence_type: IMP
  original_reference_id: PMID:12093361
  qualifier: involved_in
  review:
    summary: >-
      Independent mutant-phenotype (IMP) evidence for involvement in protein
      N-linked glycosylation. A second CDG-Ig patient with reduced ALG12
      mannosyltransferase activity shows partial loss of N-glycan side chains on
      serum transferrin, rescued by wild-type ALG12.
    action: ACCEPT
    reason: >-
      Experimentally supported core biological process, independently
      corroborating PMID:11983712.
    supported_by:
    - reference_id: PMID:12093361
      supporting_text: >-
        the partial loss of complete N-glycan
- term:
    id: GO:0006488
    label: dolichol-linked oligosaccharide biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:11983712
  qualifier: involved_in
  review:
    summary: >-
      Mutant-phenotype (IMP) evidence for involvement in dolichol-linked
      oligosaccharide biosynthesis. Loss of ALG12 blocks addition of the eighth
      mannose onto the LLO precursor; wild-type gene transduction normalizes the
      phenotype.
    action: ACCEPT
    reason: >-
      Experimentally supported core biological process (the direct step ALG12
      catalyzes in LLO assembly).
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        deficient in their capacity to add the eighth mannose residue onto the
- term:
    id: GO:0006488
    label: dolichol-linked oligosaccharide biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:12093361
  qualifier: involved_in
  review:
    summary: >-
      Independent mutant-phenotype (IMP) evidence for involvement in
      dolichol-linked oligosaccharide biosynthesis. Reduced ALG12 activity causes
      accumulation of the Man7GlcNAc2-PP-Dol intermediate.
    action: ACCEPT
    reason: >-
      Experimentally supported core biological process, corroborating the other
      IMP/IDA annotations.
    supported_by:
    - reference_id: PMID:12093361
      supporting_text: >-
        leading to the accumulation of Man(7)GlcNAc(2)-PP-Dol, which was transferred to
- term:
    id: GO:0052917
    label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
  evidence_type: IMP
  original_reference_id: PMID:11983712
  qualifier: enables
  review:
    summary: >-
      Mutant-phenotype (IMP) evidence for the specific Dol-P-Man-dependent
      alpha-1,6-mannosyltransferase activity. The CDG-Ig patient's fibroblasts
      cannot add the eighth mannose, and the human ALG12 cDNA rescues the defect,
      identifying ALG12 as this enzyme.
    action: ACCEPT
    reason: >-
      Experimentally supported core molecular function; the exact current GOA MF
      term for ALG12.
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
- term:
    id: GO:0052917
    label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
  evidence_type: IMP
  original_reference_id: PMID:12093361
  qualifier: enables
  review:
    summary: >-
      Independent mutant-phenotype (IMP) evidence for the Dol-P-Man-dependent
      mannosyltransferase activity. Patient fibroblasts show severely reduced
      Dol-P-Man:Man7GlcNAc2-PP-Dol mannosyltransferase activity, normalized by
      wild-type ALG12 expression.
    action: ACCEPT
    reason: >-
      Experimentally supported core molecular function, independently
      corroborating PMID:11983712.
    supported_by:
    - reference_id: PMID:12093361
      supporting_text: >-
        Retroviral expression of the wild-type
- term:
    id: GO:0000030
    label: mannosyltransferase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-446198
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) mannosyltransferase activity. Correct but overly general:
      the specific and experimentally supported activity is the Dol-P-Man-dependent
      alpha-1,6-mannosyltransferase GO:0052917.
    action: MODIFY
    reason: >-
      Too general. ALG12's activity is captured precisely by GO:0052917; replace
      the generic mannosyltransferase term with the specific one.
    proposed_replacement_terms:
    - id: GO:0052917
      label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
- term:
    id: GO:0000030
    label: mannosyltransferase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-4720497
  qualifier: enables
  review:
    summary: >-
      Reactome (TAS) mannosyltransferase activity (from the defective-ALG12
      disease reaction). Same over-general term as R-HSA-446198.
    action: MODIFY
    reason: >-
      Too general; the specific activity term GO:0052917 should be used.
    proposed_replacement_terms:
    - id: GO:0052917
      label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-4720497
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) location in the ER membrane. Consistent with all other
      ER-membrane evidence.
    action: ACCEPT
    reason: >-
      Correct subcellular location.
    supported_by:
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:19946888
  qualifier: located_in
  review:
    summary: >-
      High-throughput proteomics (HDA) detection of ALG12 in a membrane fraction
      from an NK-like cell line. The generic "membrane" term adds no information
      beyond the specific ER membrane localization.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Uninformative generic membrane term from a large-scale membrane-proteome
      survey (1843 proteins); the specific, well-supported location is ER
      membrane. Not incorrect, but over-broad and non-core.
    supported_by:
    - reference_id: PMID:19946888
      supporting_text: >-
        identified 1843 proteins with high confidence scores
- term:
    id: GO:0006488
    label: dolichol-linked oligosaccharide biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:11983712
  qualifier: acts_upstream_of_or_within
  review:
    summary: >-
      Direct-assay (IDA) evidence that ALG12 acts within dolichol-linked
      oligosaccharide biosynthesis, with the acts_upstream_of_or_within
      qualifier. The eighth mannose addition step ALG12 catalyzes is directly
      demonstrated by the biochemical defect and its rescue.
    action: ACCEPT
    reason: >-
      Experimentally supported core biological process.
    supported_by:
    - reference_id: PMID:11983712
      supporting_text: >-
        deficient in their capacity to add the eighth mannose residue onto the
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-446198
  qualifier: located_in
  review:
    summary: >-
      Reactome (TAS) location in the ER membrane. Consistent with all other
      ER-membrane evidence.
    action: ACCEPT
    reason: >-
      Correct subcellular location.
    supported_by:
    - reference_id: file:human/ALG12/ALG12-uniprot.txt
      supporting_text: >-
        SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: NAS
  original_reference_id: PMID:12217961
  qualifier: located_in
  review:
    summary: >-
      Non-traceable author statement (NAS) placing ALG12 in the endoplasmic
      reticulum. Broader than the ER membrane term but correct; ALG12 is an ER
      alpha-1,6-mannosyltransferase.
    action: ACCEPT
    reason: >-
      Correct but less specific than the ER membrane annotations; retained as an
      accurate broader location.
    supported_by:
    - reference_id: PMID:12217961
      supporting_text: >-
        we describe a deficiency in the ALG12 ER
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: NAS
  original_reference_id: PMID:12217961
  qualifier: involved_in
  review:
    summary: >-
      Non-traceable author statement (NAS) associating ALG12 with protein
      folding. ALG12 is a mannosyltransferase that builds the N-glycan precursor;
      N-glycosylation supports downstream glycoprotein folding/quality control,
      but ALG12 does not itself carry out protein folding. This mislabels the
      molecular role.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Over-annotation via a downstream/indirect consequence. ALG12's direct role
      is dolichol-linked oligosaccharide biosynthesis for N-glycosylation
      (GO:0006488, GO:0006487); "protein folding" is an indirect effect and does
      not describe ALG12's function. Non-core.
    supported_by:
    - reference_id: PMID:12217961
      supporting_text: >-
        N-linked glycans are first
core_functions:
- description: >-
    Dol-P-Man-dependent alpha-1,6-mannosyltransferase that adds the eighth
    mannose from dolichyl-phosphate-mannose in an alpha-1,6 linkage onto
    Man7GlcNAc2-PP-dolichol to produce Man8GlcNAc2-PP-dolichol in the ER lumen
    (EC 2.4.1.260).
  molecular_function:
    id: GO:0052917
    label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-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:11983712
    supporting_text: >-
      dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl alpha6-mannosyltransferase that is
  - reference_id: PMID:11983712
    supporting_text: >-
      deficient in their capacity to add the eighth mannose residue onto the
- description: >-
    ER membrane mannosyltransferase that contributes the eighth mannose of the
    dolichol-linked oligosaccharide precursor transferred en bloc to asparagine
    residues during protein N-linked glycosylation.
  molecular_function:
    id: GO:0052917
    label: dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-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:12093361
    supporting_text: >-
      Deficiency of the endoplasmic reticulum enzyme dolichyl-phosphate mannose
  - reference_id: PMID:12093361
    supporting_text: >-
      the partial loss of complete N-glycan
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:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:11983712
  title: Congenital disorders of glycosylation type Ig is defined by a deficiency
    in dolichyl-P-mannose:Man7GlcNAc2-PP-dolichyl mannosyltransferase.
  findings:
  - statement: >-
      Human ALG12, the ortholog of yeast ALG12, encodes the
      dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl alpha6-mannosyltransferase; CDG-Ig
      patient fibroblasts are deficient in adding the eighth mannose onto the LLO
      precursor, and the defect (F142V) is rescued by wild-type ALG12.
    supporting_text: >-
      deficient in their capacity to add the eighth mannose residue onto the
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; primary paper establishing human ALG12 identity, the
      Dol-P-Man-dependent alpha-1,6-mannosyltransferase activity, LLO
      biosynthesis role, and CDG-Ig disease. Abstract-only in cache.
- id: PMID:12093361
  title: Deficiency of dolichyl-P-Man:Man7GlcNAc2-PP-dolichyl mannosyltransferase
    causes congenital disorder of glycosylation type Ig.
  findings:
  - statement: >-
      A second CDG-Ig patient shows severely reduced ER Dol-P-Man:Man7GlcNAc2-PP-Dol
      mannosyltransferase activity with accumulation of Man7GlcNAc2-PP-Dol and
      partial loss of N-glycan side chains; wild-type ALG12 normalizes activity.
    supporting_text: >-
      leading to the accumulation of Man(7)GlcNAc(2)-PP-Dol, which was transferred to
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; independent confirmation of ALG12 mannosyltransferase
      activity, LLO role, and CDG-Ig. Abstract-only in cache.
- id: PMID:12217961
  title: ALG12 mannosyltransferase defect in congenital disorder of glycosylation
    type lg.
  findings:
  - statement: >-
      Describes deficiency in the ALG12 ER alpha-1,6-mannosyltransferase; ER
      lumenal LLO context; yeast alg12 complementation confirms enzyme identity;
      defines CDG-Ig.
    supporting_text: >-
      we describe a deficiency in the ALG12 ER
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; supports ER localization, lumenal topology, and the
      alpha-1,6-mannosyltransferase activity. Abstract-only in cache.
- id: PMID:19946888
  title: Defining the membrane proteome of NK cells.
  findings:
  - statement: >-
      Large-scale membrane-proteome survey of an NK-like cell line detecting
      ALG12 among 1843 proteins; basis of the generic membrane annotation only.
    supporting_text: >-
      identified 1843 proteins with high confidence scores
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: >-
      PubMed-verified; high-throughput proteomics providing only generic membrane
      localization, not gene-specific function.
- 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-446198
  title: ALG12 transfers Man to N-glycan precursor (GlcNAc)2 (Man)7 (PP-Dol)1
  findings: []
- id: Reactome:R-HSA-4720497
  title: Defective ALG12 does not add mannose to the N-glycan precursor
  findings: []
- id: file:human/ALG12/ALG12-uniprot.txt
  title: UniProtKB Q9BV10 (ALG12_HUMAN) curated entry
  findings:
  - statement: >-
      ALG12 is an ER membrane, multi-pass Dol-P-Man-dependent
      alpha-1,6-mannosyltransferase (EC 2.4.1.260) of the glycosyltransferase 22
      family that adds the eighth mannose onto Man7GlcNAc2-PP-dolichol in the ER
      lumen; defects cause CDG type Ig.
    supporting_text: >-
      adds the eighth mannose residue in an alpha-1,6 linkage onto