CLDN11

protein-coding

claudin 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]

Previous symbols:
  • OTM

MANE transcript

NM_005602.6

Inheritance

AD, AR

ClinVar variants

U:16B:5

Top phenotype

Leukodystrophy, hypomyelinating, 22

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr3:170,418,868-170,454,733

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~35.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

leukodystrophy, hypomyelinating, 22STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0025701

Submitter: Labcorp Genetics (formerly Invitae)

leukodystrophy, hypomyelinating, 22MODERATE

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)

Leukodystrophy, hypomyelinating, 22AR

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

Refs: 33313762Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLDN11 variants in ClinVar

5 Conditions Cataloged
not providedTotal: 9
not specifiedTotal: 9
Leukodystrophy, hypomyelinating, 22Total: 4
Marfanoid habitus and intellectual disabilityTotal: 1
CLDN11-related conditionTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
4
clinvar
1
clinvar
6
missense
14
clinvar
14
nonsense
0
start loss
1
clinvar
1
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00164121
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005602.6RefSeqNP_005593.23MANE Select
ENST00000064724.8EnsemblENSP00000064724.43MANE Select
NM_001185056.2RefSeqNP_001171985.12Standard
ENST00000970096.1EnsemblENSP00000640155.13Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.76721280.5620.000008001296
Missense (PolyPhen)2858.0960.48196600
Synonymous0.8845058.60.8530.00000399463
Loss of Function2.5807.780.003.36e-777

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.