myopathy caused by variation in POMT1
disease diseaseOn this page
Also known as myopathy caused by mutation in POMT1POMT1 myopathyPOMT1-related myopathy
Summary
myopathy caused by variation in POMT1 (MONDO:0700070) is a disease caused by POMT1 (GenCC Strong), with 1 cohort gene.
At a glance
- Causal gene: POMT1 (GenCC Strong)
- Cohort genes: 1
- ClinVar variants: 3
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | myopathy caused by variation in POMT1 |
| Mondo ID | MONDO:0700070 |
| GARD | 0026343 |
| Is cancer (heuristic) | no |
Also known as: myopathy caused by mutation in POMT1 · POMT1 myopathy · POMT1-related myopathy
Data availability: 3 ClinVar variants · 1 GenCC gene-disease record.
Disease family
An umbrella term covering 3 Mondo subtypes.
Classification path: disease › human disease › disease by body system or component › musculoskeletal system disorder › muscle tissue disorder › skeletal muscle disorder › myopathy › myopathy caused by variation in POMT1
Related subtypes (31): polyglucosan body myopathy, muscular atrophy, myopathy of extraocular muscle, acute quadriplegic myopathy, myofascial pain syndrome, myopathy with abnormal lipid metabolism, proximal myopathy with focal depletion of mitochondria, Brody myopathy, rippling muscle disease, myopathy due to myoadenylate deaminase deficiency, proximal myopathy with extrapyramidal signs, intermediate nemaline myopathy, hereditary inclusion-body myopathy, hereditary continuous muscle fiber activity, congenital myopathy, muscular dystrophy, metabolic myopathy, myositis disease, collagen 6-related myopathy, myopathy caused by variation in CRPPA, drug-induced myopathy, myopathy caused by variation in FKRP, myopathy caused by variation in FKTN, myopathy caused by variation in POMGNT1, myopathy caused by variation in POMGNT2, myopathy caused by variation in POMT2, myopathy caused by variation in GMPPB, FHL1-related myopathy, myopathy, sarcoplasmic body, myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis 2, myopathy with myalgia, increased serum creatine kinase, and with or without episodic rhabdomyolysis
Subtypes (3): muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1, autosomal recessive limb-girdle muscular dystrophy type 2K, muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1
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
3 retrieved; paginated sample, class counts are floors:
1 uncertain significance, 1 pathogenic/likely pathogenic, 1 pathogenic
| ClinVar | Variant (HGVS) | Gene | Classification | Review |
|---|---|---|---|---|
| 580081 | NM_001077365.2(POMT1):c.1272+2T>C | POMT1 | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
| 95468 | NM_001077365.2(POMT1):c.727C>T (p.Arg243Ter) | POMT1 | Pathogenic | criteria provided, multiple submitters, no conflicts |
| 498220 | NM_001077365.2(POMT1):c.1598C>T (p.Ala533Val) | POMT1 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
Genes & proteins
Mendelian disease overlap and somatic drivers
GenCC: 12 · Orphanet: 6 · 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 |
|---|---|---|---|---|
| POMT1 | Strong | Autosomal recessive | myopathy caused by variation in POMT1 | 12 |
Orphanet rare-disease linkage (cohort genes)
| Gene | Orphanet ID | Rare disease |
|---|---|---|
| POMT1 | Orphanet:370959 | Congenital muscular dystrophy with cerebellar involvement |
| POMT1 | Orphanet:370968 | Congenital muscular dystrophy with intellectual disability |
| POMT1 | Orphanet:370980 | Congenital muscular dystrophy without intellectual disability |
| POMT1 | Orphanet:588 | Muscle-eye-brain disease |
| POMT1 | Orphanet:86812 | POMT1-related limb-girdle muscular dystrophy R11 |
| POMT1 | Orphanet:899 | Walker-Warburg syndrome |
Cohort genes → proteins
1 cohort genes, 1 distinct canonical proteins.
Evidence partition
| Subset | Genes |
|---|---|
| multi_evidence | 1 |
Cohort genes (full)
| Symbol | HGNC | Ensembl | UniProt | Name | Evidence |
|---|---|---|---|---|---|
| POMT1 | HGNC:9202 | ENSG00000130714 | Q9Y6A1 | Protein O-mannosyl-transferase 1 | gencc,clinvar |
Cohort function summary
Lead sentence per gene, UniProt-curated.
| Symbol | Protein name | Function (lead sentence) |
|---|---|---|
| POMT1 | Protein O-mannosyl-transferase 1 | Transfers mannosyl residues to the hydroxyl group of serine or threonine residues. |
Protein-family classification
Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0
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 | 12.0× | 0.083 |
Per-gene assignment
| Symbol | Family | Druggable? | EC | InterPro (top 3) |
|---|---|---|---|---|
| POMT1 | Enzyme (other) | yes | 2.4.1.109 | ArnT-like_N, MIR_motif, PMT-like |
Expression context
Cohort genes with no expression data: 0.
1 cohort gene 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) | 1 |
| unknown | 0 |
Top tissues across cohort
| Tissue | Cohort genes |
|---|---|
| cerebellar cortex | 1 |
| cerebellar hemisphere | 1 |
| right hemisphere of cerebellum | 1 |
Per-gene tissue summary (top 30)
| Symbol | Bgee breadth | FANTOM5 breadth | SCXA | Top tissues |
|---|---|---|---|---|
| POMT1 | 264 | ubiquitous | marker | right hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex |
Protein interactions among cohort
Intra-cohort edges: 0.
Hub genes (top 10 by interactor count)
| Symbol | Interactor count |
|---|---|
| POMT1 | 1,475 |
Structural data
PDB: 0 · AlphaFold-only: 1 · No structure: 0
AlphaFold-only cohort genes (top 30 by pLDDT)
| Symbol | UniProt | pLDDT |
|---|---|---|
| POMT1 | Q9Y6A1 | 88.09 |
Function
Pathway analysis
Distinct Reactome pathways touched by cohort: 6. Enrichment computed across 1 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.
| Pathway | Cohort genes | Fold | FDR | Sample cohort genes |
|---|---|---|---|---|
| Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 | 1 | 3806.7× | 6e-04 | POMT1 |
| Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 | 1 | 3806.7× | 6e-04 | POMT1 |
| DAG1 core M1 glycosylations | 1 | 2855.0× | 6e-04 | POMT1 |
| DAG1 core M2 glycosylations | 1 | 2284.0× | 6e-04 | POMT1 |
| DAG1 core M3 glycosylations | 1 | 1903.3× | 6e-04 | POMT1 |
| Regulation of CDH1 posttranslational processing and trafficking to plasma membrane | 1 | 335.9× | 0.003 | POMT1 |
GO biological processes by enrichment
Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.
| GO term | Cohort genes | Fold | FDR | Sample cohort genes |
|---|---|---|---|---|
| protein O-linked glycosylation via mannose | 1 | 936.2× | 0.003 | POMT1 |
| protein O-linked glycosylation | 1 | 224.7× | 0.007 | POMT1 |
| extracellular matrix organization | 1 | 122.1× | 0.008 | POMT1 |
Therapeutics
Drug target analysis
Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1
Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).
Top cohort targets by molecule count
| Symbol | Molecules | Max phase |
|---|---|---|
| POMT1 | 0 | 0 |
Bioactivity and enzyme data
Enzyme cohort genes (≥1 EC): 1.
Cohort enzymes (BRENDA EC)
| Symbol | EC numbers | Names |
|---|---|---|
| POMT1 | 2.4.1.109 | dolichyl-phosphate-mannose-protein mannosyltransferase |
Pharmacogenomics
Cohort genes with a PharmGKB record: 1; 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 | POMT1 |
| E | Difficult family or no structure, no drug | 0 |
Undrugged target profiles
1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).
| Symbol | ChEMBL assays | Drugged partners (top 3) |
|---|---|---|
| POMT1 | 0 | — |
Clinical trials & evidence
Clinical trials
Clinical trials: 0.
Related Atlas pages
- Cohort genes: POMT1