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

Gene ID: 80781, updated on 5-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
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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)

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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_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.