GLDN
protein-codinggliomedin
Gene summary
This gene encodes a protein that contains olfactomedin-like and collagen-like domains. The encoded protein, which exists in both transmembrane and secreted forms, promotes formation of the nodes of Ranvier in the peripheral nervous system. Mutations in this gene cause a form of lethal congenital contracture syndrome in human patients. Autoantibodies to the encoded protein have been identified in sera form patients with multifocal motor neuropathy. [provided by RefSeq, May 2017]
- COLM
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~66.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014965
Submitter: ClinGen
GLDN encodes gliomedin, a Schwann cell–secreted adhesion protein required for the initiation and stabilization of nodes of Ranvier through interactions with axonal Neurofascin-186 (NF186) and Schwann cell NrCAM. This process is essential for clustering sodium channels and establishing normal peripheral nerve conduction. The gene–disease association was first established by Maluenda et al., (PMID: 27616481) who identified biallelic GLDN variants in individuals with fetal akinesia and congenital contractures. Since the initial description, multiple unrelated families have been reported with nonsense, frameshift, canonical splice, and missense variants segregating with disease in an autosomal recessive pattern. Many pathogenic variants localize to the conserved extracellular olfactomedin domain critical for NF186 binding (PMIDs: 28726266, 35806855, 39713852). Multiple recurrent and non-recurrent variants comprising missense, nonsense, frameshift, and splice variants have been reported in affected individuals, some of which segregated with disease in multiple affected individuals within families. Variants from more than 10 independent publications have been scored as part of this curation and the maximum score for genetic evidence (+12pts) has been reached. The mechanism of pathogenicity is loss of function, and in vitro studies demonstrate that pathogenic GLDN variants impair gliomedin trafficking to the cell surface and abolish NF186 binding (PMID: 27616481). Mouse models lacking gliomedin show disrupted Schwann cell microvilli organization and failure of early sodium channel clustering at heminodes without defects in myelination (PMID: 20188654). Double knockout mice lacking both gliomedin and NrCAM show nodal defects and motor abnormalities closely mirroring the human phenotype (PMID: 24719088). Prenatal ultrasound findings commonly include polyhydramnios, decreased or absent fetal movements, arthrogryposis multiplex congenita, fixed limb joints, short long bones, hydrops fetalis, and pulmonary hypoplasia, with detection often late in gestation (mean 30-32 weeks) (PMID: 35806855). Outcomes include neonatal death, elective termination, or survival with significant respiratory and neuromuscular morbidity. Although initially described as uniformly lethal, later reports demonstrate phenotypic variability, with survival beyond infancy and into adolescence documented in a subset of individuals receiving intensive supportive care (PMIDs: 35806855, 39713852). These observations support a continuous phenotypic spectrum rather than distinct disease entities. In summary, the Prenatal Gene Curation Expert Panel concludes that GLDN has DEFINITIVE evidence for autosomal recessive Lethal Congenital Contracture Syndrome 11. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Prenatal GCEP on the meeting date 11/18/2025 (SOP Version 11).
Inheritance Pattern: AR
Disease ID:MONDO:0014965
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014965
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0014965
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014965
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Neurologic; Musculoskeletal
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 GLDN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_181789.4. 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 | 14 | 2 | 16 | |||
| missense | 13 | 97 | 13 | 2 | 125 | |
| nonsense | 1 | 7 | 8 | |||
| start loss | 0 | |||||
| frameshift | 3 | 7 | 1 | 11 | ||
| splice donor/acceptor (+/-2bp) | 1 | 4 | 3 | 1 | 9 | |
| Total | 5 | 31 | 101 | 28 | 4 | 169 |
Highest pathogenic variant AF is 0.00007627112
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_861454.2 | 10 | MANE Select | |
| Ensembl | ENSP00000335196.6 | 10 | MANE Select | |
| RefSeq | NP_001317226.1 | 9 | Standard | |
| Ensembl | ENSP00000379681.2 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- microvillus organization
- heterotypic cell-cell adhesion
- clustering of voltage-gated sodium channels
Molecular Function
- protein binding involved in heterotypic cell-cell adhesion
Cellular Component
- collagen trimer
- extracellular space
- plasma membrane
- integral component of membrane
- axon
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000335449
- Coding exons
- 10
- Length
- 66385
- Individuals with no LoFs
- 125675
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 73
- Defined
- 125748
- p
- 0.000290
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.130 | 303 | 297 | 1.02 | 0.0000145 | 3529 |
| Missense (PolyPhen) | 95 | 100.63 | 0.94405 | 1204 | ||
| Synonymous | -1.07 | 133 | 118 | 1.13 | 0.00000654 | 1109 |
| Loss of Function | 0.525 | 21 | 23.8 | 0.884 | 0.00000124 | 283 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00020 | 0.00018 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.00053 | 0.00052 | rare |
| Other | 0.00052 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ligand for NRCAM and NFASC/neurofascin that plays a role in the formation and maintenance of the nodes of Ranvier on myelinated axons. Mediates interaction between Schwann cell microvilli and axons via its interactions with NRCAM and NFASC. Nodes of Ranvier contain clustered sodium channels that are crucial for the saltatory propagation of action potentials along myelinated axons. During development, nodes of Ranvier are formed by the fusion of two heminodes. Required for normal clustering of sodium channels at heminodes; not required for the formation of mature nodes with normal sodium channel clusters. Required, together with NRCAM, for maintaining NFASC and sodium channel clusters at mature nodes of Ranvier. {ECO:0000250|UniProtKB:Q8BMF8}.;
- Disease
- DISEASE: Lethal congenital contracture syndrome 11 (LCCS11) [MIM:617194]: A form of lethal congenital contracture syndrome, an autosomal recessive disorder characterized by degeneration of anterior horn neurons, extreme skeletal muscle atrophy and congenital non-progressive joint contractures. The contractures can involve the upper or lower limbs and/or the vertebral column, leading to various degrees of flexion or extension limitations evident at birth. {ECO:0000269|PubMed:27616481}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- LoFtool
- 0.263
- RVIS EVS
- 1.42
- RVIS percentile EVS
- 94.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.110
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |