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GLDN gliomedin [ Homo sapiens (human) ]

Gene ID: 342035, updated on 3-Apr-2024

Summary

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Official Symbol
GLDNprovided by HGNC
Official Full Name
gliomedinprovided by HGNC
Primary source
HGNC:HGNC:29514
See related
Ensembl:ENSG00000186417 MIM:608603; AllianceGenome:HGNC:29514
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLOM; COLM; CRGL2; CRG-L2; LCCS11; UNC-112; UNC-122
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]
Expression
Biased expression in brain (RPKM 4.5), fat (RPKM 3.3) and 12 other tissues See more
Orthologs
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Genomic context

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See GLDN in Genome Data Viewer
Location:
15q21.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (51341655..51413365)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (49149425..49221133)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (51633852..51700197)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene cytochrome P450 family 19 subfamily A member 1 Neighboring gene CYP19A1 promoter I.4 Neighboring gene uncharacterized LOC112268146 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:51621311-51621511 Neighboring gene microRNA 7973-2 Neighboring gene microRNA 7973-1 Neighboring gene CYP19A1 promoter I.1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:51678296-51678796 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:51682661-51683516 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:51741640-51742839 Neighboring gene Dmx like 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:51861014-51861520 Neighboring gene Sharpr-MPRA regulatory region 1269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6432 Neighboring gene uncharacterized LOC105370816 Neighboring gene CRISPRi-validated cis-regulatory element chr15.1149

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The latest FADS: Functional analysis of GLDN patient variants and classification of GLDN-associated AMC as a type of viable fetal akinesia deformation sequence. Mis EK, et al. Am J Med Genet A, 2020 Oct. PMID 32812332
  2. Survival among children with "Lethal" congenital contracture syndrome 11 caused by novel mutations in the gliomedin gene (GLDN). Wambach JA, et al. Hum Mutat, 2017 Nov. PMID 28726266, Free PMC Article
  3. The olfactomedin domain from gliomedin is a β-propeller with unique structural properties. Han H, et al. J Biol Chem, 2015 Feb 6. PMID 25525261, Free PMC Article
  4. Autoantibodies to neurofascin-186 and gliomedin in multifocal motor neuropathy. Notturno F, et al. J Neuroimmunol, 2014 Nov 15. PMID 25283719
  5. Secreted gliomedin is a perinodal matrix component of peripheral nerves. Eshed Y, et al. J Cell Biol, 2007 May 7. PMID 17485493, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The latest FADS: Functional analysis of GLDN patient variants and classification of GLDN-associated AMC as a type of viable fetal akinesia deformation sequence.
    Title: The latest FADS: Functional analysis of GLDN patient variants and classification of GLDN-associated AMC as a type of viable fetal akinesia deformation sequence.
  2. Our findings expand the genotypic and phenotypic spectrum of LCCS11 and demonstrate that the condition may not necessarily be lethal in the neonatal period.
    Title: Survival among children with "Lethal" congenital contracture syndrome 11 caused by novel mutations in the gliomedin gene (GLDN).
  3. data indicate that mutations of GLDN or CNTNAP1 (MIM: 616286), encoding essential components of the nodes of Ranvier and paranodes, respectively, lead to inherited nodopathies, a distinct disease entity among peripheral neuropathies
    Title: Mutations in GLDN, Encoding Gliomedin, a Critical Component of the Nodes of Ranvier, Are Responsible for Lethal Arthrogryposis.
  4. gliomedin, NF186, and contactin are novel target antigens in Guillain-Barre syndrome
    Title: Nodal proteins are target antigens in Guillain-Barré syndrome.
  5. Fibronectin type III-like domains of neurofascin-186 protein mediate gliomedin binding and its clustering at the developing nodes of Ranvier
    Title: Fibronectin type III-like domains of neurofascin-186 protein mediate gliomedin binding and its clustering at the developing nodes of Ranvier.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Lethal congenital contracture syndrome 11
MedGen: C4310670 OMIM: 617194 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study of sex hormones, gonadotropins and sex hormone-binding protein in Chinese men.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Markers

Homology

Clone Names

  • FLJ23917

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding involved in heterotypic cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in clustering of voltage-gated sodium channels IEA
Inferred from Electronic Annotation
more info
  
involved_in heterotypic cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
  
involved_in microvillus organization IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
  
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cell surface IDA
Inferred from Direct Assay
more info
 PubMed 
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
gliomedin
Names
collomin
colmedin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_054933.1 RefSeqGene

    Range
    5140..71485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001330297.2 → NP_001317226.1  gliomedin isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' terminal exon, resulting in a different 5' UTR and the use of a downstream start codon, compared to variant 1. The encoded isoform (2) may undergo proteolytic processing similar to isoform 1, but it has a shorter N-terminus and lacks a putative furin cleavage site compared to isoform 1.
    Source sequence(s)
    AC020891, BC113397, BX101284, BX538105
    Consensus CDS
    CCDS81882.1
    UniProtKB/TrEMBL
    Q14DE1
    Related
    ENSP00000379681.2, ENST00000396399.6

  2. NM_181789.4 → NP_861454.2  gliomedin isoform 1 precursor

    See identical proteins and their annotated locations for NP_861454.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1), which undergoes proteolytic processing to generate a secreted form of the protein.
    Source sequence(s)
    AC020891, BK001262, BX101284
    Consensus CDS
    CCDS10140.2
    UniProtKB/Swiss-Prot
    Q6UXZ7, Q6ZMI3, Q7Z359
    Related
    ENSP00000335196.6, ENST00000335449.11
    Conserved Domains (2) summary
    pfam01391
    Location:160 → 217
    Collagen; Collagen triple helix repeat (20 copies)
    pfam02191
    Location:304 → 542
    OLF; Olfactomedin-like domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    51341655..51413365
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022125.1 → XP_016877614.1  gliomedin isoform X5

  2. XM_017022121.2 → XP_016877610.1  gliomedin isoform X1

  3. XM_017022126.3 → XP_016877615.1  gliomedin isoform X6

  4. XM_017022124.3 → XP_016877613.1  gliomedin isoform X3

    UniProtKB/TrEMBL
    Q14DE1

  5. XM_017022122.3 → XP_016877611.1  gliomedin isoform X3

    UniProtKB/TrEMBL
    Q14DE1

  6. XM_011521501.3 → XP_011519803.1  gliomedin isoform X2

    UniProtKB/TrEMBL
    Q14DE1
    Conserved Domains (2) summary
    pfam01391
    Location:40 → 97
    Collagen; Collagen triple helix repeat (20 copies)
    pfam02191
    Location:184 → 422
    OLF; Olfactomedin-like domain

  7. XM_047432431.1 → XP_047288387.1  gliomedin isoform X3

  8. XM_047432433.1 → XP_047288389.1  gliomedin isoform X4

  9. XM_047432432.1 → XP_047288388.1  gliomedin isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    49149425..49221133
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377813.1 → XP_054233788.1  gliomedin isoform X5

  2. XM_054377808.1 → XP_054233783.1  gliomedin isoform X1

  3. XM_054377814.1 → XP_054233789.1  gliomedin isoform X6

  4. XM_054377811.1 → XP_054233786.1  gliomedin isoform X3

  5. XM_054377810.1 → XP_054233785.1  gliomedin isoform X3

  6. XM_054377809.1 → XP_054233784.1  gliomedin isoform X2

  7. XM_054377812.1 → XP_054233787.1  gliomedin isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZMI3.1 GenPept UniProtKB/Swiss-Prot:Q6ZMI3

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