muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13

disease

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Also known as MDDGA13muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13

Summary

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (MONDO:0014120) is a disease caused by B4GAT1 (GenCC Strong), with 2 cohort genes.

At a glance

Causal gene: B4GAT1 (GenCC Strong)
Cohort genes: 2
ClinVar variants: 201

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13
Mondo ID	MONDO:0014120
OMIM	615287
DOID	DOID:0111238
UMLS	C3809042
MedGen	815372
GARD	0015938
Is cancer (heuristic)	no

Also known as: MDDGA13 · muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13

Data availability: 201 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › congenital nervous system disorder › congenital muscular dystrophy › muscular dystrophy-dystroglycanopathy › muscular dystrophy-dystroglycanopathy, type A › muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13

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

201 retrieved; paginated sample, class counts are floors:

100 likely benign, 85 uncertain significance, 7 conflicting classifications of pathogenicity, 3 pathogenic, 3 benign/likely benign, 1 pathogenic/likely pathogenic, 1 benign, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
51008	NM_006876.2(B4GAT1):[c.1168A>G;c.1217C>T]		Pathogenic	no assertion criteria provided
1252009	NM_006876.3(B4GAT1):c.1207G>T (p.Glu403Ter)	B4GAT1	Pathogenic	no assertion criteria provided
1709842	NM_006876.3(B4GAT1):c.864T>A (p.Tyr288Ter)	B4GAT1	Pathogenic	criteria provided, single submitter
183334	NM_006876.3(B4GAT1):c.821_822insTT (p.Glu274fs)	B4GAT1	Pathogenic/Likely pathogenic	no assertion criteria provided
4849376	NM_006876.3(B4GAT1):c.686_690del (p.Asp229fs)	B4GAT1	Likely pathogenic	criteria provided, single submitter
3897434	NM_006876.3(B4GAT1):c.948C>T (p.Ala316=)	B4GAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
421636	NM_006876.3(B4GAT1):c.196G>A (p.Ala66Thr)	B4GAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
507234	NM_006876.3(B4GAT1):c.1056+6C>G	B4GAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
541281	NM_006876.3(B4GAT1):c.1146C>G (p.Phe382Leu)	B4GAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
573749	NM_006876.3(B4GAT1):c.758C>G (p.Thr253Ser)	B4GAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
581531	NM_006876.3(B4GAT1):c.355C>A (p.Pro119Thr)	B4GAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
755187	NM_006876.3(B4GAT1):c.185A>G (p.Gln62Arg)	B4GAT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1006470	NM_006876.3(B4GAT1):c.748dup (p.Trp250fs)	B4GAT1	Uncertain significance	criteria provided, single submitter
1009820	NM_006876.3(B4GAT1):c.780C>G (p.Phe260Leu)	B4GAT1	Uncertain significance	criteria provided, single submitter
1017612	NM_006876.3(B4GAT1):c.796C>T (p.Arg266Cys)	B4GAT1	Uncertain significance	criteria provided, single submitter
1019556	NM_006876.3(B4GAT1):c.151C>T (p.Pro51Ser)	B4GAT1	Uncertain significance	criteria provided, single submitter
1019557	NM_006876.3(B4GAT1):c.223G>A (p.Ala75Thr)	B4GAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
1021545	NM_006876.3(B4GAT1):c.512G>C (p.Arg171Pro)	B4GAT1	Uncertain significance	criteria provided, single submitter
1057113	NM_006876.3(B4GAT1):c.679G>A (p.Asp227Asn)	B4GAT1	Uncertain significance	criteria provided, single submitter
1064288	NM_006876.3(B4GAT1):c.952G>A (p.Val318Met)	B4GAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
1195055	NM_006876.3(B4GAT1):c.76C>A (p.Gln26Lys)	B4GAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
1304862	NM_006876.3(B4GAT1):c.447G>T (p.Met149Ile)	B4GAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
1307190	NM_006876.3(B4GAT1):c.338T>C (p.Leu113Pro)	B4GAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
1346739	NM_006876.3(B4GAT1):c.128A>G (p.Asp43Gly)	B4GAT1	Uncertain significance	criteria provided, single submitter
1350891	NM_006876.3(B4GAT1):c.478C>G (p.Pro160Ala)	B4GAT1	Uncertain significance	criteria provided, single submitter
1357657	NM_006876.3(B4GAT1):c.144C>A (p.Phe48Leu)	B4GAT1	Uncertain significance	criteria provided, single submitter
1369250	NM_006876.3(B4GAT1):c.271G>A (p.Asp91Asn)	B4GAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
1387762	NM_006876.3(B4GAT1):c.838C>A (p.Gln280Lys)	B4GAT1	Uncertain significance	criteria provided, single submitter
1396950	NM_006876.3(B4GAT1):c.1240C>T (p.Arg414Cys)	B4GAT1	Uncertain significance	criteria provided, multiple submitters, no conflicts
1397777	NM_006876.3(B4GAT1):c.667G>A (p.Ala223Thr)	B4GAT1	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 1 · 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.

Gene	Classification	Inheritance	Disease	Records
B4GAT1	Strong	Autosomal recessive	muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	3
B3GNT2	Moderate	Autosomal recessive	muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	2

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
B4GAT1	Orphanet:899	Walker-Warburg syndrome

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
B4GAT1	HGNC:15685	ENSG00000174684	O43505	Beta-1,4-glucuronyltransferase 1	gencc,clinvar
B3GNT2	HGNC:15629	ENSG00000170340	Q9NY97	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2	gencc

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
B4GAT1	Beta-1,4-glucuronyltransferase 1	Beta-1,4-glucuronyltransferase involved in O-mannosylation of alpha-dystroglycan (DAG1).
B3GNT2	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2	Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.5

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.

Family	Genes	Fold	FDR
Enzyme (other)	1	6.0×	0.320
Other/Unknown	1	0.9×	0.805

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
B4GAT1	Enzyme (other)	yes	2.4.1.149	B4GAT1
B3GNT2	Other/Unknown	no		Glyco_trans_31

Expression context

Cohort genes with no expression data: 0.

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

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
endothelial cell	1
middle temporal gyrus	1
pons	1
oocyte	1
secondary oocyte	1
visceral pleura	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
B4GAT1	285	ubiquitous	marker	endothelial cell, middle temporal gyrus, pons
B3GNT2	272	ubiquitous	marker	secondary oocyte, oocyte, visceral pleura

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
B3GNT2	1,709
B4GAT1	823

Structural data

PDB: 1 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
B3GNT2	Q9NY97	12

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
B4GAT1	O43505	88.46

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 15. Enrichment computed across 2 evidence-associated genes (2 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 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Keratan sulfate/keratin metabolism	2	496.5×	5e-05	B4GAT1, B3GNT2
Keratan sulfate biosynthesis	2	380.7×	5e-05	B4GAT1, B3GNT2
Glycosaminoglycan metabolism	2	219.6×	1e-04	B4GAT1, B3GNT2
O-linked glycosylation	2	144.6×	2e-04	B4GAT1, B3GNT2
Metabolism of carbohydrates and carbohydrate derivatives	2	120.2×	2e-04	B4GAT1, B3GNT2
Defective LARGE causes MDDGA6 and MDDGB6	1	1903.3×	0.001	B4GAT1
Matriglycan biosynthesis on DAG1	1	407.9×	0.005	B4GAT1
Post-translational protein modification	2	19.2×	0.005	B4GAT1, B3GNT2
Metabolism of proteins	2	12.4×	0.011	B4GAT1, B3GNT2
Metabolism	2	11.6×	0.011	B4GAT1, B3GNT2
Diseases associated with O-glycosylation of proteins	1	107.7×	0.013	B4GAT1
O-linked glycosylation of mucins	1	92.1×	0.014	B3GNT2
Diseases of glycosylation	1	65.6×	0.018	B4GAT1
Diseases of metabolism	1	40.2×	0.026	B4GAT1
Disease	1	6.5×	0.147	B4GAT1

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
keratan sulfate proteoglycan biosynthetic process	2	991.3×	7e-06	B4GAT1, B3GNT2
axon guidance	2	90.6×	4e-04	B4GAT1, B3GNT2
poly-N-acetyllactosamine biosynthetic process	1	1053.2×	0.002	B3GNT2
protein O-linked glycosylation via mannose	1	468.1×	0.004	B4GAT1
protein O-linked glycosylation	1	112.3×	0.012	B3GNT2
cellular response to leukemia inhibitory factor	1	79.5×	0.013	B3GNT2
sensory perception of smell	1	78.0×	0.013	B3GNT2

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 1 of 2 evidence-associated genes (50%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
B4GAT1	0	0
B3GNT2	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
B3GNT2	1	Binding:1

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
B4GAT1	2.4.1.149	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; 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):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	1	B4GAT1
E	Difficult family or no structure, no drug	1	B3GNT2

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
B4GAT1	0	—
B3GNT2	1	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: B4GAT1, B3GNT2