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.
| 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.
Proposed replacements:
dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
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.
Proposed replacements:
dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity
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
|
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.
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.
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