ALG12-congenital disorder of glycosylation

disease
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Also known as ALG12-CDGALG12-CDG (CDG-Ig)carbohydrate deficient glycoprotein syndrome type IgCDG 1GCDG syndrome type IgCDG-IgCDG1GCDGIgcongenital disorder of glycosylation type 1gcongenital disorder of glycosylation type Igcongenital disorder of glycosylation, type Igmannosyltransferase 8 deficiency

Summary

ALG12-congenital disorder of glycosylation (MONDO:0011783) is a disease caused by ALG12 (GenCC Definitive), with 5 cohort genes.

At a glance

  • Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Causal gene: ALG12 (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 520
  • Phenotypes (HPO): 93

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families11WorldwideValidated
Point prevalence<1 / 1 000 000WorldwideValidated

Signs & symptoms

Clinical features (HPO)

93 HPO clinical features (Orphanet curated; top 50 by frequency):

HPO IDTermFrequency
HP:0012379Abnormal enzyme/coenzyme activityObligate (100%)
HP:0000119Abnormality of the genitourinary systemVery frequent (80-99%)
HP:0003256Abnormality of the coagulation cascadeVery frequent (80-99%)
HP:0000253Progressive microcephalyFrequent (30-79%)
HP:0000750Delayed speech and language developmentFrequent (30-79%)
HP:0000759Abnormal peripheral nervous system morphologyFrequent (30-79%)
HP:0001249Intellectual disabilityFrequent (30-79%)
HP:0001252HypotoniaFrequent (30-79%)
HP:0001508Failure to thriveFrequent (30-79%)
HP:0001929Reduced factor XI activityFrequent (30-79%)
HP:0002011Morphological central nervous system abnormalityFrequent (30-79%)
HP:0002194Delayed gross motor developmentFrequent (30-79%)
HP:0002205Recurrent respiratory infectionsFrequent (30-79%)
HP:0002257Chronic rhinitisFrequent (30-79%)
HP:0003645Prolonged partial thromboplastin timeFrequent (30-79%)
HP:0004855Reduced protein S activityFrequent (30-79%)
HP:0005543Reduced protein C activityFrequent (30-79%)
HP:0006532Recurrent pneumoniaFrequent (30-79%)
HP:0008151Prolonged prothrombin timeFrequent (30-79%)
HP:0010976Decreased total B cell countFrequent (30-79%)
HP:0011968Feeding difficultiesFrequent (30-79%)
HP:0040246Reduced antithrombin antigenFrequent (30-79%)
HP:0100776Recurrent pharyngitisFrequent (30-79%)
HP:0410018Recurrent ear infectionsFrequent (30-79%)
HP:0410242Abnormal IgG levelFrequent (30-79%)
HP:0001622Premature birthOccasional (5-29%)
HP:0001762Talipes equinovarusOccasional (5-29%)
HP:0001792Small nailOccasional (5-29%)
HP:0001852Sandal gapOccasional (5-29%)
HP:0001873ThrombocytopeniaOccasional (5-29%)
HP:0001988Recurrent hypoglycemiaOccasional (5-29%)
HP:0001999Abnormal facial shapeOccasional (5-29%)
HP:0002020Gastroesophageal refluxOccasional (5-29%)
HP:0002079Hypoplasia of the corpus callosumOccasional (5-29%)
HP:0002119VentriculomegalyOccasional (5-29%)
HP:0002162Low posterior hairlineOccasional (5-29%)
HP:0002389Cavum septum pellucidumOccasional (5-29%)
HP:0002650ScoliosisOccasional (5-29%)
HP:0002910Elevated circulating hepatic transaminase concentrationOccasional (5-29%)
HP:0003026Short long boneOccasional (5-29%)
HP:0003049Ulnar deviation of the wristOccasional (5-29%)
HP:0003073HypoalbuminemiaOccasional (5-29%)
HP:0003146HypocholesterolemiaOccasional (5-29%)
HP:0004209Clinodactyly of the 5th fingerOccasional (5-29%)
HP:0009623Proximal placement of thumbOccasional (5-29%)
HP:0010557Overlapping fingersOccasional (5-29%)
HP:0011327Posterior plagiocephalyOccasional (5-29%)
HP:0011344Severe global developmental delayOccasional (5-29%)
HP:0011471Gastrostomy tube feeding in infancyOccasional (5-29%)
HP:0011800Midface retrusionOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical nameALG12-congenital disorder of glycosylation
Mondo IDMONDO:0011783
MeSHC535745
OMIM607143
Orphanet79324
DOIDDOID:0080559
NCITC126873
SNOMED CT711155008
UMLSC2931001
MedGen443954
GARD0009833
Is cancer (heuristic)no

Also known as: ALG12-CDG · ALG12-CDG (CDG-Ig) · ALG12-congenital disorder of glycosylation · carbohydrate deficient glycoprotein syndrome type Ig · CDG 1G · CDG syndrome type Ig · CDG-Ig · CDG1G · CDGIg · congenital disorder of glycosylation type 1g · congenital disorder of glycosylation type Ig · congenital disorder of glycosylation, type Ig · mannosyltransferase 8 deficiency

Data availability: 520 ClinVar variants · 5 GenCC gene-disease records · 2 cell lines.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseaseinborn errors of metabolismcongenital disorder of glycosylationcongenital disorder of glycosylation type IALG12-congenital disorder of glycosylation

Related subtypes (27): PMM2-congenital disorder of glycosylation, developmental and epileptic encephalopathy, 36, SSR4-congenital disorder of glycosylation, ALG3-congenital disorder of glycosylation, MPI-congenital disorder of glycosylation, ALG6-congenital disorder of glycosylation 1C, ALG2-congenital disorder of glycosylation, DPAGT1-congenital disorder of glycosylation, ALG8-congenital disorder of glycosylation, ALG1-congenital disorder of glycosylation, ALG9-congenital disorder of glycosylation, congenital disorder of glycosylation type 1E, MPDU1-congenital disorder of glycosylation, DK1-congenital disorder of glycosylation, RFT1-congenital disorder of glycosylation, SRD5A3-congenital disorder of glycosylation, DPM3-congenital disorder of glycosylation, ALG11-congenital disorder of glycosylation, DDOST-congenital disorder of glycosylation, PGM1-congenital disorder of glycosylation, congenital muscular dystrophy with intellectual disability and severe epilepsy, STT3A-congenital disorder of glycosylation, STT3B-congenital disorder of glycosylation, developmental and epileptic encephalopathy, 50, congenital disorder of glycosylation, type IAA, congenital disorder of glycosylation, type ICC, SSR3-CDG

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

520 retrieved; paginated sample, class counts are floors:

225 likely benign, 193 uncertain significance, 32 conflicting classifications of pathogenicity, 24 pathogenic, 19 benign, 13 likely pathogenic, 7 pathogenic/likely pathogenic, 7 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
4724NM_019109.5(ALG1):c.773C>T (p.Ser258Leu)ALG1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1069034NM_024105.4(ALG12):c.1156dup (p.Gln386fs)ALG12Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1383200NM_024105.4(ALG12):c.522G>A (p.Trp174Ter)ALG12Pathogeniccriteria provided, single submitter
1440773NM_024105.4(ALG12):c.789C>A (p.Tyr263Ter)ALG12Pathogeniccriteria provided, single submitter
1448154NM_024105.4(ALG12):c.502G>T (p.Glu168Ter)ALG12Pathogeniccriteria provided, single submitter
1456464NM_024105.4(ALG12):c.688dup (p.Tyr230fs)ALG12Pathogeniccriteria provided, single submitter
2073899NM_024105.4(ALG12):c.336G>A (p.Trp112Ter)ALG12Pathogeniccriteria provided, single submitter
2090231NM_024105.4(ALG12):c.1129C>T (p.Gln377Ter)ALG12Pathogeniccriteria provided, single submitter
2103386NM_024105.4(ALG12):c.424_428delinsCAGTTCCAC (p.Phe142fs)ALG12Pathogeniccriteria provided, single submitter
2138458NM_024105.4(ALG12):c.30del (p.Leu12fs)ALG12Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2426800NC_000022.10:g.(?50297486)(50307413_?)delALG12Pathogeniccriteria provided, single submitter
242854NM_024105.4(ALG12):c.1001del (p.Asn334fs)ALG12Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
242855NM_024105.4(ALG12):c.117del (p.Gln40fs)ALG12Pathogeniccriteria provided, multiple submitters, no conflicts
2626751NM_024105.4(ALG12):c.768+1dupALG12Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2697267NM_024105.4(ALG12):c.698_699del (p.Arg233fs)ALG12Pathogeniccriteria provided, single submitter
2734803NM_024105.4(ALG12):c.731G>A (p.Trp244Ter)ALG12Pathogeniccriteria provided, single submitter
2824299NM_024105.4(ALG12):c.160C>T (p.Gln54Ter)ALG12Pathogeniccriteria provided, single submitter
2839616NM_024105.4(ALG12):c.21_33dup (p.Leu12fs)ALG12Pathogeniccriteria provided, single submitter
3358165NM_024105.4(ALG12):c.604C>T (p.Arg202Ter)ALG12Pathogeniccriteria provided, single submitter
3434NM_024105.4(ALG12):c.200C>T (p.Thr67Met)ALG12Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3435NM_024105.4(ALG12):c.437G>A (p.Arg146Gln)ALG12Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3437NM_024105.4(ALG12):c.473T>C (p.Leu158Pro)ALG12Pathogenicno assertion criteria provided
3438NM_024105.4(ALG12):c.1242C>G (p.Tyr414Ter)ALG12Pathogenicno assertion criteria provided
3617623NM_024105.4(ALG12):c.755del (p.Ser252fs)ALG12Pathogeniccriteria provided, single submitter
3688618NM_024105.4(ALG12):c.1015_1016del (p.Trp339fs)ALG12Pathogeniccriteria provided, single submitter
4697444NM_024105.4(ALG12):c.861del (p.Thr288fs)ALG12Pathogeniccriteria provided, single submitter
4767896NM_024105.4(ALG12):c.904_908del (p.Tyr302fs)ALG12Pathogeniccriteria provided, single submitter
560937NM_024105.4(ALG12):c.930_931del (p.Arg311fs)ALG12Pathogeniccriteria provided, multiple submitters, no conflicts
987881NM_024105.4(ALG12):c.165C>A (p.Tyr55Ter)ALG12Pathogeniccriteria provided, single submitter
1031734NM_007347.5(AP4E1):c.3313C>T (p.Arg1105Ter)AP4E1Pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
ALG12DefinitiveAutosomal recessiveALG12-congenital disorder of glycosylation5

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ALG12Orphanet:79324ALG12-CDG
ALG1Orphanet:79327ALG1-CDG
AP4E1Orphanet:280763Severe intellectual disability and progressive spastic paraplegia

Cohort genes → proteins

5 cohort genes, 5 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
ALG12HGNC:19358ENSG00000182858Q9BV10Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferasegencc,clinvar
BRD1HGNC:1102ENSG00000100425O95696Bromodomain-containing protein 1clinvar
ALG1HGNC:18294ENSG00000033011Q9BT22Chitobiosyldiphosphodolichol beta-mannosyltransferaseclinvar
AP4E1HGNC:573ENSG00000081014Q9UPM8AP-4 complex subunit epsilon-1clinvar
PLXNB2HGNC:9104ENSG00000196576O15031Plexin-B2clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ALG12Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferaseMannosyltransferase that operates in the biosynthetic pathway of dolichol-linked oligosaccharides, the glycan precursors employed in protein asparagine (N)-glycosylation.
BRD1Bromodomain-containing protein 1Scaffold subunit of various histone acetyltransferase (HAT) complexes, such as the MOZ/MORF and HBO1 complexes, that acts as a regulator of hematopoiesis.
ALG1Chitobiosyldiphosphodolichol beta-mannosyltransferaseMannosyltransferase that operates in the biosynthetic pathway of dolichol-linked oligosaccharides, the glycan precursors employed in protein asparagine (N)-glycosylation.
AP4E1AP-4 complex subunit epsilon-1Component of the adaptor protein complex 4 (AP-4).
PLXNB2Plexin-B2Cell surface receptor for SEMA4C, SEMA4D and SEMA4G that plays an important role in cell-cell signaling.

Protein-family classification

Druggable: 3 · Difficult: 1 · Unknown: 1 · Druggable fraction: 0.6

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Enzyme (other)24.8×0.235
Antibody/Immunoglobulin15.8×0.320
Transcription factor11.6×0.634
Other/Unknown10.4×0.983

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
ALG12Enzyme (other)yes2.4.1.260GPI_mannosylTrfase
BRD1Transcription factornoPWWP_dom, Bromodomain, Znf_PHD
ALG1Enzyme (other)yes2.4.1.142Glyco_trans_1, ALG1-like
AP4E1Other/UnknownnoClathrin/coatomer_adapt-like_N, ARM-like, ARM-type_fold
PLXNB2Antibody/ImmunoglobulinyesSemap_dom, Plexin_repeat, IPT_dom

Expression context

Cohort genes with no expression data: 0.

4 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)5
unknown0

Top tissues across cohort

TissueCohort genes
stromal cell of endometrium2
buccal mucosa cell2
left lobe of thyroid gland1
right lobe of thyroid gland1
oocyte1
paraflocculus1
secondary oocyte1
body of pancreas1
esophagus squamous epithelium1
gingival epithelium1
lower esophagus mucosa1
metanephros cortex1
right uterine tube1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
ALG12217ubiquitousmarkerright lobe of thyroid gland, stromal cell of endometrium, left lobe of thyroid gland
BRD1289ubiquitousmarkeroocyte, secondary oocyte, paraflocculus
ALG1185ubiquitousmarkerstromal cell of endometrium, buccal mucosa cell, body of pancreas
AP4E1262ubiquitousyesgingival epithelium, esophagus squamous epithelium, buccal mucosa cell
PLXNB2276ubiquitousmarkerright uterine tube, metanephros cortex, lower esophagus mucosa

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
BRD12,359
ALG12,187
AP4E12,108
PLXNB21,606
ALG121,385

Intra-cohort edges

ABSources
ALG1ALG12string_interaction

Structural data

PDB: 3 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
BRD1O95696318
AP4E1Q9UPM84
PLXNB2O150311

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
ALG12Q9BV1093.26
ALG1Q9BT2293.24

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 24. Enrichment computed across 5 evidence-associated genes (4 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Diseases associated with N-glycosylation of proteins2317.2×3e-04ALG12, ALG1
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein2103.8×0.002ALG12, ALG1
Defective ALG1 causes CDG-1k12855.0×0.002ALG1
Defective ALG12 causes CDG-1g12855.0×0.002ALG12
Diseases of glycosylation265.6×0.002ALG12, ALG1
Diseases of metabolism240.2×0.004ALG12, ALG1
Asparagine N-linked glycosylation230.1×0.006ALG12, ALG1
Regulation of TP53 Activity through Acetylation1114.2×0.026BRD1
Lysosome Vesicle Biogenesis181.6×0.033AP4E1
trans-Golgi Network Vesicle Budding163.4×0.034AP4E1
Post-translational protein modification29.6×0.034ALG12, ALG1
Golgi Associated Vesicle Biogenesis150.1×0.040AP4E1
Regulation of TP53 Activity133.2×0.054BRD1
Disease26.5×0.054ALG12, ALG1
Metabolism of proteins26.2×0.056ALG12, ALG1
Chromatin organization120.4×0.070BRD1
HATs acetylate histones119.8×0.070BRD1
Chromatin modifying enzymes118.1×0.072BRD1
Transcriptional Regulation by TP53115.5×0.079BRD1
Membrane Trafficking19.3×0.124AP4E1
Vesicle-mediated transport18.7×0.126AP4E1
RNA Polymerase II Transcription15.6×0.181BRD1
Gene expression (Transcription)14.5×0.215BRD1
Generic Transcription Pathway13.8×0.240BRD1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
dolichol-linked oligosaccharide biosynthetic process2337.0×4e-04ALG12, ALG1
protein N-linked glycosylation2105.3×0.002ALG12, ALG1
regulation of developmental process1481.5×0.023BRD1
regulation of hemopoiesis1306.4×0.024BRD1
excitatory synapse assembly1259.3×0.024PLXNB2
regulation of protein phosphorylation1224.7×0.024PLXNB2
erythrocyte maturation1168.5×0.025BRD1
response to immobilization stress1146.5×0.025BRD1
response to electrical stimulus1129.6×0.025BRD1
regulation of neuron migration1124.8×0.025PLXNB2
positive regulation of axonogenesis1116.2×0.025PLXNB2
regulation of GTPase activity1102.1×0.025PLXNB2
positive regulation of erythrocyte differentiation1102.1×0.025BRD1
semaphorin-plexin signaling pathway180.2×0.026PLXNB2
negative regulation of cell adhesion176.6×0.026PLXNB2
protein targeting173.3×0.026AP4E1
neuroblast proliferation173.3×0.026PLXNB2
synapse assembly146.2×0.037PLXNB2
positive regulation of translation145.5×0.037PLXNB2
receptor-mediated endocytosis144.4×0.037PLXNB2
neural tube closure137.5×0.042PLXNB2
regulation of cell migration131.5×0.047PLXNB2
homophilic cell-cell adhesion128.1×0.049PLXNB2
positive regulation of neuron projection development127.4×0.049PLXNB2
regulation of cell shape124.6×0.053PLXNB2
intracellular protein localization120.9×0.058AP4E1
protein folding120.7×0.058ALG12
vesicle-mediated transport119.3×0.060AP4E1
brain development115.9×0.070PLXNB2
chromatin remodeling114.6×0.073BRD1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 5

Druggability breadth: 2 of 5 evidence-associated genes (40%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
ALG1200
BRD100
ALG100
AP4E100
PLXNB200

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
BRD1121Binding:118, Functional:3
ALG11Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ALG122.4.1.260dolichyl-P-Man:Man7GlcNAc2-PP-dolichol alpha-1,6-mannosyltransferase
ALG12.4.1.142chitobiosyldiphosphodolichol beta-mannosyltransferase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
BRD1121

Pharmacogenomics

Cohort genes with a PharmGKB record: 5; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1PLXNB2
DDruggable family + AlphaFold only, no drug2ALG12, ALG1
EDifficult family or no structure, no drug2BRD1, AP4E1

Undrugged target profiles

5 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
BRD1121
ALG120
ALG11
AP4E10
PLXNB20

Clinical trials & evidence

Clinical trials

Clinical trials: 0.