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    GLDN gliomedin [ Homo sapiens (human) ]

    Gene ID: 342035, updated on 28-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (51341655..51413365)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (49149425..49221133)
    RS_2024_09 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 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. 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
    2. 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
    3. Autoantibodies to neurofascin-186 and gliomedin in multifocal motor neuropathy. Notturno F, et al. J Neuroimmunol, 2014 Nov 15. PMID 25283719
    4. 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
    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
    		not available

    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_2024_08

    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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