CLDN11
protein-codingclaudin 11, the group of MicroRNA protein coding host genes|Claudins
Gene summary
This gene encodes a member of the claudin family. Claudins are integral membrane proteins and components of tight junction strands. Tight junction strands serve as a physical barrier to prevent solutes and water from passing freely through the paracellular space between epithelial or endothelial cell sheets, and also play critical roles in maintaining cell polarity and signal transductions. The protein encoded by this gene is a major component of central nervous system (CNS) myelin and plays an important role in regulating proliferation and migration of oligodendrocytes. Mouse studies showed that the gene deficiency results in deafness and loss of the Sertoli cell epithelial phenotype in the testis. This protein is a tight junction protein at the human blood-testis barrier (BTB), and the BTB disruption is related to a dysfunction of this gene. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Aug 2010]
- OTM
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~35.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0025701
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0025701
Submitter: ClinGen
CLDN11: Hypomyelinating Leukodystrophy 22, autosomal dominant CLDN11 was first associated with autosomal dominant hypomyelinating leukodystrophy 22 (HLD22) in 2021 (OMIM 619328, PMID 33313762). HLD22 is characterized by early-onset spastic movement disorders, expressive speech disorders, and eye abnormalities, as well as hypomyelination in the brain. Affected individuals have borderline intellectual disability, dysarthria, drooling, lower limb hyperreflexia, lower and upper limb hypertonia. Additional features often include delayed milestones including speech and language development and ability to sit and/or walk, as well as eye findings including astigmatism, hypermetropia, nystagmus, and strabismus. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found a consistent phenotype and no difference in molecular mechanism or inheritance pattern; therefore, the single disease entity of HLD22 has been maintained. The CLDN11 gene encodes claudin 11, also known as oligodendrocyte transmembrane protein (OTM) or oligodendrocyte specific protein (OSP). Claudin 11 is a member of the claudin tight junction family, which plays a structural role in the radial component of the myelin sheath, acting as a diffusion barrier. Two stop-loss variants have been reported in 3 probands across 1 publication (PMID 33313762). All variants occurred de novo in the affected individuals. The mechanism of pathogenicity is not well understood; at the protein level, the de novo stop-loss variants occur in the last exon (exon 3) and are predicted to lead to an extension of 39 amino acids to the cytoplasmic C-terminus of claudin-11 (PMID 33313762). The gene-disease relationship is also supported by experimental evidence. CLDN11 is highly expressed specifically in oligodendrocytes and early oligodendrocyte progenitor cells (PMID 10797530). Claudin-11 knockout mice exhibit hindlimb weakness and absent tight junction strands in optic nerves, which mirror the neurologic and visual phenotype in affected patients (PMID: 10612400). Cultured cells with mutated CLDN11 demonstrated decreased morphological differentiation and decreased expression of oligodendroglial differentiation marker proteins PLP1 and MBP (PMID 41752091). In summary, there is moderate evidence supporting the relationship between CLDN11 and autosomal dominant hypomyelinating leukodystrophy 22, also known as CLDN11-related hypomyelinating leukodystrophy. This classification was approved by the ClinGen Leukodystrophy and Leukoencephalopathy GCEP on the meeting date of March 5, 2025 (SOP Version 12).
Clinical Genomic Database (CGD)
Manifestation: Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CLDN11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005602.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 4 | 1 | 6 | ||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 16 | 4 | 1 | 21 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005593.2 | 3 | MANE Select | |
| Ensembl | ENSP00000064724.4 | 3 | MANE Select | |
| RefSeq | NP_001171985.1 | 2 | Standard | |
| Ensembl | ENSP00000640155.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell adhesion molecules (CAMs) - Homo sapiens (human)
- Tight junction - Homo sapiens (human)
- Hepatitis C - Homo sapiens (human)
- Leukocyte transendothelial migration - Homo sapiens (human)
- Ectoderm Differentiation
Biological Process
- calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules
Molecular Function
- structural molecule activity
- protein binding
- identical protein binding
Cellular Component
- plasma membrane
- bicellular tight junction
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000064724
- Coding exons
- 3
- Length
- 441517
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.76 | 72 | 128 | 0.562 | 0.00000800 | 1296 |
| Missense (PolyPhen) | 28 | 58.096 | 0.48196 | 600 | ||
| Synonymous | 0.884 | 50 | 58.6 | 0.853 | 0.00000399 | 463 |
| Loss of Function | 2.58 | 0 | 7.78 | 0.00 | 3.36e-7 | 77 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium- independent cell-adhesion activity. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.269
Intolerance Scores
- LoFtool
- 0.115
- RVIS EVS
- -0.19
- RVIS percentile EVS
- 39.68
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.507
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |