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

    Gene ID: 85301, updated on 14-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (114154098..114312511)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (126352719..126511655)
    RS_2024_09 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 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. Mutations in COL27A1 cause Steel syndrome and suggest a founder mutation effect in the Puerto Rican population. Gonzaga-Jauregui C, et al. Eur J Hum Genet, 2015 Mar. PMID 24986830, 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 (31) 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
    		Compare labs

    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)

    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 extracellular matrix organization 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 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_2024_08

    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

    Gene LinkOut

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