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    COL18A1 collagen type XVIII alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 80781, updated on 1-Mar-2024

    Summary

    Official Symbol
    COL18A1provided by HGNC
    Official Full Name
    collagen type XVIII alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2195
    See related
    Ensembl:ENSG00000182871 MIM:120328; AllianceGenome:HGNC:2195
    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
    KS; KNO; GLCC; KNO1
    Summary
    This gene encodes the alpha chain of type XVIII collagen. This collagen is one of the multiplexins, extracellular matrix proteins that contain multiple triple-helix domains (collagenous domains) interrupted by non-collagenous domains. A long isoform of the protein has an N-terminal domain that is homologous to the extracellular part of frizzled receptors. Proteolytic processing at several endogenous cleavage sites in the C-terminal domain results in production of endostatin, a potent antiangiogenic protein that is able to inhibit angiogenesis and tumor growth. Mutations in this gene are associated with Knobloch syndrome. The main features of this syndrome involve retinal abnormalities, so type XVIII collagen may play an important role in retinal structure and in neural tube closure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
    Annotation information
    Annotation category: suggests misassembly
    Expression
    Ubiquitous expression in liver (RPKM 68.9), kidney (RPKM 46.2) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL18A1 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (45405165..45513720)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43770922..43881831)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (46825080..46933634)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46790350-46790860 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46796710-46796898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46799692-46800692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46800693-46801692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46808325-46809136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46812138-46812638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46824235-46824935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46827875-46828666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46828667-46829459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46833102-46833725 Neighboring gene COL18A1 antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46834349-46834972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46834973-46835596 Neighboring gene MT-CO1 pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46838464-46839218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46839219-46839973 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46839974-46840729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46841485-46842239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46844008-46844605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46844606-46845204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46847276-46847948 Neighboring gene COL18A1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46850948-46851946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46851947-46852943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46854143-46854992 Neighboring gene uncharacterized LOC124905042 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46858777-46859506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46859507-46860236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46860237-46860966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46862147-46862656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46870853-46871354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46871355-46871854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46874827-46875383 Neighboring gene breast cancer associated ESR1 regulating natural antisense transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46885741-46886304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46885176-46885740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46894762-46895262 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46908672-46909202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46912122-46912622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46934825-46935332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46935840-46936346 Neighboring gene microRNA 6815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18591 Neighboring gene Sharpr-MPRA regulatory region 1559 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46948644-46948814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46954106-46954980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46962482-46962994 Neighboring gene solute carrier family 19 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13403 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46970045-46970201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46975660-46976554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46980259-46980968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46998853-46999354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47001008-47001944 Neighboring gene uncharacterized LOC107985485 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47009554-47010054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47015623-47016124 Neighboring gene Sharpr-MPRA regulatory region 7423 Neighboring gene MPRA-validated peak4424 silencer Neighboring gene MPRA-validated peak4426 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47031725-47032226 Neighboring gene long intergenic non-protein coding RNA 1694 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:47053121-47054320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47057095-47057612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13411 Neighboring gene poly(rC) binding protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47204393-47205264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47236921-47237422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47237423-47237922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47241669-47242354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47244540-47245132 Neighboring gene MPRA-validated peak4427 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47255439-47255946 Neighboring gene PCBP3 antisense RNA 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Glaucoma, primary closed-angle
    MedGen: C5394374 OMIM: 618880 GeneReviews: Not available
    Compare labs
    Knobloch syndrome 1
    MedGen: C4551775 OMIM: 267750 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Multiple loci influencing hippocampal degeneration identified by genome scan.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ27325, FLJ34914, MGC74745

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in animal organ morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endothelial cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of cell population proliferation TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in notochord development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to hydrostatic pressure IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in visual perception TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    collagen alpha-1(XVIII) chain
    Names
    antiangiogenic agent
    collagen, type XVIII, alpha 1
    endostatin
    multi-functional protein MFP

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_011903.1 RefSeqGene

      Range
      5001..113529
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001379500.1NP_001366429.1  collagen alpha-1(XVIII) chain isoform 4 preproprotein

      Status: REVIEWED

      Source sequence(s)
      BX322561, BX322562
      Consensus CDS
      CCDS42971.1
      Related
      ENSP00000498485.1, ENST00000651438.1
    2. NM_030582.4NP_085059.2  collagen alpha-1(XVIII) chain isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_085059.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as NCI-493) uses an alternate splice donor in the 5' terminal exon compared to variant 3. The encoded isoform (1) is shorter than isoform 3.
      Source sequence(s)
      AF018082, BC063833, BX322561
      Consensus CDS
      CCDS42972.1
      UniProtKB/Swiss-Prot
      A8MVI4, P39060, Q58EX6, Q6RZ39, Q6RZ40, Q6RZ41, Q8N4S4, Q8WXI5, Q96T70, Q9UK38, Q9Y6Q7, Q9Y6Q8
      Related
      ENSP00000347665.5, ENST00000355480.10
      Conserved Domains (4) summary
      pfam01391
      Location:822872
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:221409
      TSPN; Thrombospondin N-terminal -like domains
      cd00247
      Location:13401510
      Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...
      pfam06121
      Location:25194
      DUF959; Domain of Unknown Function (DUF959)
    3. NM_130444.3NP_569711.2  collagen alpha-1(XVIII) chain isoform 3 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as NCI-728) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      AF018082, BC063833, BX322561
      Consensus CDS
      CCDS77643.1
      UniProtKB/Swiss-Prot
      A8MVI4, P39060, Q58EX6, Q6RZ39, Q6RZ40, Q6RZ41, Q8N4S4, Q8WXI5, Q96T70, Q9UK38, Q9Y6Q7, Q9Y6Q8
      Related
      ENSP00000352798.4, ENST00000359759.8
      Conserved Domains (5) summary
      cd07455
      Location:330452
      CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )
      pfam01391
      Location:10571107
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:456644
      TSPN; Thrombospondin N-terminal -like domains
      cd00247
      Location:15751745
      Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...
      pfam06121
      Location:25194
      DUF959; Domain of Unknown Function (DUF959)

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      45405165..45513720
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791815.1 Reference GRCh38.p14 PATCHES

      Range
      22400..130946
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      43770922..43881831
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_130445.4: Suppressed sequence

      Description
      NM_130445.4: This RefSeq was removed by NCBI staff. Please email info@ncbi.nlm.nih.gov for more information.