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COL27A1 collagen type XXVII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 85301, updated on 5-Mar-2024

Summary

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Official Symbol
COL27A1provided by HGNC
Official Full Name
collagen type XXVII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:22986
See related
Ensembl:ENSG00000196739 MIM:608461; AllianceGenome:HGNC:22986
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
STLS
Summary
This gene encodes a member of the fibrillar collagen family, and plays a role during the calcification of cartilage and the transition of cartilage to bone. The encoded protein product is a preproprotein. It includes an N-terminal signal peptide, which is followed by an N-terminal propetide, mature peptide and a C-terminal propeptide. The N-terminal propeptide contains thrombospondin N-terminal-like and laminin G-like domains. The mature peptide is a major triple-helical region. The C-terminal propeptide, also known as COLFI domain, plays crucial roles in tissue growth and repair. Mutations in this gene cause Steel syndrome. Alternatively spliced transcript variants have been found, but the full-length nature of some variants has not been determined. [provided by RefSeq, Sep 2014]
Expression
Ubiquitous expression in endometrium (RPKM 17.8), prostate (RPKM 8.1) and 23 other tissues See more
Orthologs
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Genomic context

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See COL27A1 in Genome Data Viewer
Location:
9q32
Exon count:
66
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (114154098..114312511)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (126352719..126511655)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (116917817..117074791)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987120 Neighboring gene uncharacterized LOC124902251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116861361-116861896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116875188-116875688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116875689-116876189 Neighboring gene Sharpr-MPRA regulatory region 2704 Neighboring gene kinesin family member 12 Neighboring gene uncharacterized LOC105376225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116915624-116916145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20209 Neighboring gene Sharpr-MPRA regulatory region 14358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116925428-116925944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116978156-116978656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116980984-116981982 Neighboring gene NANOG hESC enhancer GRCh37_chr9:116986380-116986932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116994231-116994732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116994733-116995232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116997162-116997662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116997663-116998163 Neighboring gene microRNA 455 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_106356 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:117038878-117040077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:117043569-117044381 Neighboring gene uncharacterized LOC124902252 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:117050487-117051686 Neighboring gene uncharacterized LOC105376224 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:117068890-117069390 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:117069391-117069891 Neighboring gene Sharpr-MPRA regulatory region 10745 Neighboring gene orosomucoid 1 Neighboring gene orosomucoid 2 Neighboring gene AT-hook transcription factor

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. Bioinformatics Analysis and Experimental Verification Identify Downregulation of COL27A1 in Poor Segmental Congenital Scoliosis. Hu Z, et al. Comput Math Methods Med, 2022. PMID 35186112, Free PMC Article
  2. Brothers with novel compound heterozygous mutations in COL27A1 causing dental and genital abnormalities. Satoh C, et al. Eur J Med Genet, 2021 Feb. PMID 33359165
  3. Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide. Gonzaga-Jauregui C, et al. Eur J Hum Genet, 2020 Sep. PMID 32376988, Free PMC Article
  4. First reported case of Steel syndrome in the European population: A novel homozygous mutation in COL27A1 and review of the literature. Evie Kritioti, et al. Eur J Med Genet, 2020 Jul. PMID 32360765
  5. Three new patients with Steel syndrome and a Puerto Rican specific COL27A1 mutation. Amlie-Wolf L, et al. Am J Med Genet A, 2020 Apr. PMID 31903681

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Brothers with novel compound heterozygous mutations in COL27A1 causing dental and genital abnormalities.
    Title: Brothers with novel compound heterozygous mutations in COL27A1 causing dental and genital abnormalities.
  2. Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide.
    Title: Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide.
  3. Three new patients with Steel syndrome and a Puerto Rican specific COL27A1 mutation.
    Title: Three new patients with Steel syndrome and a Puerto Rican specific COL27A1 mutation.
  4. First reported case of Steel syndrome in the European population: A novel homozygous mutation in COL27A1 and review of the literature.
    Title: First reported case of Steel syndrome in the European population: A novel homozygous mutation in COL27A1 and review of the literature.
  5. two loci in or near GDF5 and COL27A1 that are associated with knee pain, were identified.
    Title: Genome-wide association study of knee pain identifies associations with GDF5 and COL27A1 in UK Biobank.
  6. analysis of genetic variants of COL27A1 and tenascin C in achilles tendinopathy and anterior cruciate ligament ruptures
    Title: Defining the molecular signatures of Achilles tendinopathy and anterior cruciate ligament ruptures: A whole-exome sequencing approach.
  7. Our report further validates the role of COL27A1 mutations in causation of Steel syndrome.
    Title: Second family provides further evidence for causation of Steel syndrome by biallelic mutations in COL27A1.
  8. we conclude that the novel splice-site variant identified in COL27A1 is the most likely cause for Steel syndrome in this family and that the hearing loss is part of this syndrome's phenotype
    Title: A novel aberrant splice site mutation in COL27A1 is responsible for Steel syndrome and extension of the phenotype to include hearing loss.
  9. Genetic analysis between COL27A1 and Tourette syndrome was performed.
    Title: Support of positive association in family-based genetic analysis between COL27A1 and Tourette syndrome.
  10. Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population
    Title: Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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
Steel syndrome
MedGen: C3554594 OMIM: 615155 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study of Tourette's syndrome.
EBI GWAS Catalog
Many sequence variants affecting diversity of adult human height.
EBI GWAS Catalog
Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11895, KIAA1870, MGC11337

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength HDA PubMed 
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
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 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 growth plate cartilage chondrocyte development IEA
Inferred from Electronic Annotation
more info
  
involved_in notochord development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of collagen trimer IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of fibrillar collagen trimer IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
collagen alpha-1(XXVII) chain
Names
collagen, type XXVII, alpha 1

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_034260.1 RefSeqGene

    Range
    4993..161967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_032888.4 → NP_116277.2  collagen alpha-1(XXVII) chain preproprotein

    See identical proteins and their annotated locations for NP_116277.2

    Status: REVIEWED

    Source sequence(s)
    AI808820, AL356796, AL445543, AY149237, BC035728, BU076480
    Consensus CDS
    CCDS6802.1
    UniProtKB/Swiss-Prot
    Q66K43, Q8IZC6, Q96JF7
    Related
    ENSP00000348385.3, ENST00000356083.8
    Conserved Domains (3) summary
    pfam01391
    Location:694 → 752
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:1661 → 1859
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:45 → 220
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    114154098..114312511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519138.3 → XP_011517440.1  collagen alpha-1(XXVII) chain isoform X1

    Conserved Domains (3) summary
    pfam01391
    Location:692 → 750
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:1659 → 1857
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43 → 218
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  2. XM_047423992.1 → XP_047279948.1  collagen alpha-1(XXVII) chain isoform X4

  3. XM_011519140.2 → XP_011517442.1  collagen alpha-1(XXVII) chain isoform X2

    Conserved Domains (3) summary
    pfam01391
    Location:694 → 752
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:1643 → 1841
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:45 → 220
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  4. XM_006717308.3 → XP_006717371.1  collagen alpha-1(XXVII) chain isoform X3

    Conserved Domains (3) summary
    pfam01391
    Location:676 → 734
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:1643 → 1841
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:45 → 220
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  5. XM_047423993.1 → XP_047279949.1  collagen alpha-1(XXVII) chain isoform X5

  6. XM_011519143.3 → XP_011517445.1  collagen alpha-1(XXVII) chain isoform X7

    Conserved Domains (2) summary
    pfam01391
    Location:694 → 752
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:45 → 220
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  7. XM_011519144.3 → XP_011517446.1  collagen alpha-1(XXVII) chain isoform X8

    Conserved Domains (2) summary
    pfam01391
    Location:694 → 752
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:45 → 220
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  8. XM_011519142.4 → XP_011517444.1  collagen alpha-1(XXVII) chain isoform X6

    Conserved Domains (2) summary
    pfam01391
    Location:694 → 752
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:45 → 220
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

  9. XM_017015239.2 → XP_016870728.1  collagen alpha-1(XXVII) chain isoform X9

  10. XM_047423994.1 → XP_047279950.1  collagen alpha-1(XXVII) chain isoform X10

  11. XM_047423995.1 → XP_047279951.1  collagen alpha-1(XXVII) chain isoform X12

  12. XM_006717310.4 → XP_006717373.1  collagen alpha-1(XXVII) chain isoform X11

    Conserved Domains (2) summary
    pfam09606
    Location:582 → 795
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cl02436
    Location:887 → 1087
    COLFI; Fibrillar collagen C-terminal domain

  13. XM_011519145.4 → XP_011517447.1  collagen alpha-1(XXVII) chain isoform X13

    Conserved Domains (2) summary
    pfam01391
    Location:565 → 622
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:850 → 1048
    COLFI; Fibrillar collagen C-terminal domain

RNA

  1. XR_929860.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    126352719..126511655
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364055.1 → XP_054220030.1  collagen alpha-1(XXVII) chain isoform X1

  2. XM_054364058.1 → XP_054220033.1  collagen alpha-1(XXVII) chain isoform X4

  3. XM_054364056.1 → XP_054220031.1  collagen alpha-1(XXVII) chain isoform X2

  4. XM_054364057.1 → XP_054220032.1  collagen alpha-1(XXVII) chain isoform X3

  5. XM_054364059.1 → XP_054220034.1  collagen alpha-1(XXVII) chain isoform X5

  6. XM_054364061.1 → XP_054220036.1  collagen alpha-1(XXVII) chain isoform X7

  7. XM_054364062.1 → XP_054220037.1  collagen alpha-1(XXVII) chain isoform X8

  8. XM_054364060.1 → XP_054220035.1  collagen alpha-1(XXVII) chain isoform X6

  9. XM_054364063.1 → XP_054220038.1  collagen alpha-1(XXVII) chain isoform X9

  10. XM_054364064.1 → XP_054220039.1  collagen alpha-1(XXVII) chain isoform X10

  11. XM_054364066.1 → XP_054220041.1  collagen alpha-1(XXVII) chain isoform X12

  12. XM_054364065.1 → XP_054220040.1  collagen alpha-1(XXVII) chain isoform X11

  13. XM_054364067.1 → XP_054220042.1  collagen alpha-1(XXVII) chain isoform X13

RNA

  1. XR_008488095.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032161.1: Suppressed sequence

    Description
    NM_032161.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZC6.1 GenPept UniProtKB/Swiss-Prot:Q8IZC6

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