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Aliases for GLDN Gene

Aliases for GLDN Gene

  • Gliomedin 2 3 3 5
  • Collomin 2 3
  • COLM 3 4
  • Colmedin 3
  • UNC-112 3
  • CRG-L2 3
  • LCCS11 3
  • CRGL2 3
  • CLOM 3

External Ids for GLDN Gene

Previous HGNC Symbols for GLDN Gene

  • COLM

Previous GeneCards Identifiers for GLDN Gene

  • GC15P049422
  • GC15P051633
  • GC15P028463

Summaries for GLDN Gene

Entrez Gene Summary for GLDN Gene

  • 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]

GeneCards Summary for GLDN Gene

GLDN (Gliomedin) is a Protein Coding gene. Diseases associated with GLDN include Lethal Congenital Contracture Syndrome 11 and Multifocal Motor Neuropathy. Gene Ontology (GO) annotations related to this gene include protein binding involved in heterotypic cell-cell adhesion. An important paralog of this gene is OLFML2B.

UniProtKB/Swiss-Prot for GLDN Gene

  • 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.

Additional gene information for GLDN Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GLDN Gene

Genomics for GLDN Gene

GeneHancer (GH) Regulatory Elements for GLDN Gene

Promoters and enhancers for GLDN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15I051340 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 577.3 -0.1 -70 2.2 KLF1 SIN3A ZIC2 E2F1 ZNF335 ZFHX2 PATZ1 PRDM10 KLF8 EGR2 GLDN GNB5 CYP19A1
GH15I051317 Enhancer 1 ENCODE dbSUPER 28 -22.7 -22730 2.5 MLX RAD21 THRB ZNF48 RARA CREM THAP11 MIXL1 HMG20B SP5 GLDN GNB5 ENSG00000259306 CYP19A1
GH15I051333 Enhancer 1 Ensembl ENCODE dbSUPER 27.9 -6.7 -6720 2.4 SRF RFX1 JUN NR2F1 MAX ELF1 ZFHX2 CTBP1 GATA3 RUNX3 GLDN ENSG00000259668 GNB5 CYP19A1 ENSG00000259306
GH15I051347 Enhancer 0.8 dbSUPER 32.2 +8.2 8217 5.1 PKNOX1 BATF IRF4 ATF7 ETV6 FOS BCLAF1 IKZF2 RUNX3 CBFB ENSG00000270378 GLDN GNB5
GH15I051337 Promoter/Enhancer 0.8 EPDnew ENCODE 26.8 -3.0 -2997 1.5 NFRKB CYP19A1 GLDN ENSG00000259306
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GLDN on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GLDN gene promoter:

Genomic Locations for GLDN Gene

Genomic Locations for GLDN Gene
chr15:51,341,516-51,408,013
(GRCh38/hg38)
Size:
66,498 bases
Orientation:
Plus strand
chr15:51,633,713-51,700,210
(GRCh37/hg19)

Genomic View for GLDN Gene

Genes around GLDN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GLDN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GLDN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GLDN Gene

Proteins for GLDN Gene

  • Protein details for GLDN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZMI3-GLDN_HUMAN
    Recommended name:
    Gliomedin
    Protein Accession:
    Q6ZMI3
    Secondary Accessions:
    • Q6UXZ7
    • Q7Z359

    Protein attributes for GLDN Gene

    Size:
    551 amino acids
    Molecular mass:
    58957 Da
    Quaternary structure:
    • Homotrimer (via collagen-like domains). Interacts with NRCAM and NFASC/neurofascin (PubMed:27616481). Interaction with glial NRCAM enhances interaction with axonal NFASC. Interacts with MYOC.

    Alternative splice isoforms for GLDN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GLDN Gene

Post-translational modifications for GLDN Gene

  • N-glycosylated.
  • Proteolytic proccessing by a furin-like protease causes shedding of the ectodomain. Further cleavage by BMP1 releases the olfactomedin-like domain.
  • Glycosylation at isoforms=2130, posLast=329329, posLast=357357, isoforms=2378, and posLast=464464

No data available for DME Specific Peptides for GLDN Gene

Domains & Families for GLDN Gene

Gene Families for GLDN Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for GLDN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6ZMI3

UniProtKB/Swiss-Prot:

GLDN_HUMAN :
  • The olfactomedin-like domain mediates NFASC/neurofascin and NRCAM binding.
Domain:
  • The olfactomedin-like domain mediates NFASC/neurofascin and NRCAM binding.
genes like me logo Genes that share domains with GLDN: view

Function for GLDN Gene

Molecular function for GLDN Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for GLDN Gene

Gene Ontology (GO) - Molecular Function for GLDN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0086080 protein binding involved in heterotypic cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with GLDN: view
genes like me logo Genes that share phenotypes with GLDN: view

Human Phenotype Ontology for GLDN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GLDN Gene

MGI Knock Outs for GLDN:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for GLDN Gene

Localization for GLDN Gene

Subcellular locations from UniProtKB/Swiss-Prot for GLDN Gene

Cell membrane; Single-pass type II membrane protein. Cell projection, axon. Note=Detected at the nodes of Ranvier. Detected at immature heminodes. {ECO:0000250 UniProtKB:Q80WL1}.
Gliomedin shedded ectodomain: Secreted. Secreted, extracellular space, extracellular matrix. Note=Proteolytic processing gives rise to a soluble extracellular domain that is secreted. The gliomedin shedded ectodomain localizes to the nodes of Ranvier. {ECO:0000250 UniProtKB:Q80WL1}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GLDN gene
Compartment Confidence
plasma membrane 4
extracellular 4
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for GLDN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0005615 extracellular space IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GLDN: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GLDN Gene

Pathways & Interactions for GLDN Gene

No Data Available

Interacting Proteins for GLDN Gene

Selected Interacting proteins: Q6ZMI3-GLDN_HUMAN for GLDN Gene via IID

Gene Ontology (GO) - Biological Process for GLDN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
GO:0032528 microvillus organization IEA --
GO:0034113 heterotypic cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with GLDN: view

No data available for Pathways by source and SIGNOR curated interactions for GLDN Gene

Drugs & Compounds for GLDN Gene

No Compound Related Data Available

Transcripts for GLDN Gene

Unigene Clusters for GLDN Gene

Gliomedin:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GLDN Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1:
SP2: -
SP3: - - -
SP4: - -
SP5:

Relevant External Links for GLDN Gene

GeneLoc Exon Structure for
GLDN
ECgene alternative splicing isoforms for
GLDN

Expression for GLDN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GLDN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GLDN Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x6.4), Brain - Substantia nigra (x4.8), and Nerve - Tibial (x4.3).

Protein differential expression in normal tissues from HIPED for GLDN Gene

This gene is overexpressed in Serum (64.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for GLDN Gene



Protein tissue co-expression partners for GLDN Gene

NURSA nuclear receptor signaling pathways regulating expression of GLDN Gene:

GLDN

SOURCE GeneReport for Unigene cluster for GLDN Gene:

Hs.526441

mRNA Expression by UniProt/SwissProt for GLDN Gene:

Q6ZMI3-GLDN_HUMAN
Tissue specificity: Specifically expressed in spinal cord, brain, placenta and sciatic nerve. More abundant in peripheral than central nervous system.

Evidence on tissue expression from TISSUES for GLDN Gene

  • Intestine(4.2)
  • Nervous system(3.5)
genes like me logo Genes that share expression patterns with GLDN: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for GLDN Gene

Orthologs for GLDN Gene

This gene was present in the common ancestor of animals.

Orthologs for GLDN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GLDN 33 34
  • 99.27 (n)
cow
(Bos Taurus)
Mammalia GLDN 34 33
  • 88.35 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GLDN 33 34
  • 88.11 (n)
mouse
(Mus musculus)
Mammalia Gldn 33 16 34
  • 85.95 (n)
rat
(Rattus norvegicus)
Mammalia Gldn 33
  • 83.88 (n)
oppossum
(Monodelphis domestica)
Mammalia GLDN 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GLDN 34
  • 53 (a)
OneToOne
chicken
(Gallus gallus)
Aves GLDN 33 34
  • 66.73 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 53 (a)
OneToMany
-- 34
  • 43 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia gldn 33
  • 62.21 (n)
zebrafish
(Danio rerio)
Actinopterygii gldn 33
  • 53.18 (n)
colm 34
  • 42 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG6867 34
  • 17 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea unc-122 34
  • 21 (a)
ManyToMany
cof-2 34
  • 20 (a)
ManyToMany
Species where no ortholog for GLDN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GLDN Gene

ENSEMBL:
Gene Tree for GLDN (if available)
TreeFam:
Gene Tree for GLDN (if available)

Paralogs for GLDN Gene

Paralogs for GLDN Gene

(10) SIMAP similar genes for GLDN Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with GLDN: view

Variants for GLDN Gene

Sequence variations from dbSNP and Humsavar for GLDN Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs368085516 pathogenic, Lethal congenital contracture syndrome 11 51,404,533(+) C/A/G/T coding_sequence_variant, intron_variant, missense_variant, stop_gained, synonymous_variant
rs539703340 pathogenic, Lethal congenital contracture syndrome 11 51,404,338(+) C/A/T coding_sequence_variant, intron_variant, stop_gained, synonymous_variant
rs764239923 pathogenic, Lethal congenital contracture syndrome 11, Lethal congenital contracture syndrome 11 (LCCS11) [MIM:617194] 51,404,521(+) G/A/C coding_sequence_variant, intron_variant, missense_variant
rs779432560 pathogenic, Lethal congenital contracture syndrome 11, Lethal congenital contracture syndrome 11 (LCCS11) [MIM:617194] 51,341,779(+) C/A/G/T 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs886041056 pathogenic, Lethal congenital contracture syndrome 11 51,397,535(+) CCCCC/CCCC coding_sequence_variant, frameshift

Structural Variations from Database of Genomic Variants (DGV) for GLDN Gene

Variant ID Type Subtype PubMed ID
nsv977716 CNV duplication 23825009
nsv94788 CNV insertion 16902084
nsv471243 CNV gain 18288195
nsv1047443 CNV gain 25217958
esv3636461 CNV gain 21293372
esv34532 CNV gain 17911159
esv2760031 CNV gain 17122850
dgv4526n54 CNV gain 21841781

Variation tolerance for GLDN Gene

Residual Variation Intolerance Score: 84% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.11; 90.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GLDN Gene

Human Gene Mutation Database (HGMD)
GLDN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GLDN

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GLDN Gene

Disorders for GLDN Gene

MalaCards: The human disease database

(3) MalaCards diseases for GLDN Gene - From: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
lethal congenital contracture syndrome 11
  • lccs11
multifocal motor neuropathy
  • mmn
lethal congenital contracture syndrome
  • lethal congenital contracture syndrome 1
- elite association - COSMIC cancer census association via MalaCards
Search GLDN in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GLDN_HUMAN
  • 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.

Additional Disease Information for GLDN

genes like me logo Genes that share disorders with GLDN: view

No data available for Genatlas for GLDN Gene

Publications for GLDN Gene

  1. Gliomedin mediates Schwann cell-axon interaction and the molecular assembly of the nodes of Ranvier. (PMID: 16039564) Eshed Y … Peles E (Neuron 2005) 2 3 4 22 58
  2. Mutations in GLDN, Encoding Gliomedin, a Critical Component of the Nodes of Ranvier, Are Responsible for Lethal Arthrogryposis. (PMID: 27616481) Maluenda J … Melki J (American journal of human genetics 2016) 3 4 58
  3. Secreted gliomedin is a perinodal matrix component of peripheral nerves. (PMID: 17485493) Eshed Y … Peles E (The Journal of cell biology 2007) 3 22 58
  4. Cleavage and oligomerization of gliomedin, a transmembrane collagen required for node of ranvier formation. (PMID: 17293346) Maertens B … Koch M (The Journal of biological chemistry 2007) 3 22 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for GLDN Gene

Sources for GLDN Gene

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