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    COL1A1 collagen type I alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1277, updated on 12-Feb-2024

    Summary

    Official Symbol
    COL1A1provided by HGNC
    Official Full Name
    collagen type I alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2197
    See related
    Ensembl:ENSG00000108821 MIM:120150; AllianceGenome:HGNC:2197
    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
    OI1; OI2; OI3; OI4; EDSC; CAFYD; EDSARTH1
    Summary
    This gene encodes the pro-alpha1 chains of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIA, Ehlers-Danlos syndrome Classical type, Caffey Disease and idiopathic osteoporosis. Reciprocal translocations between chromosomes 17 and 22, where this gene and the gene for platelet-derived growth factor beta are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans, resulting from unregulated expression of the growth factor. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]
    Expression
    Biased expression in gall bladder (RPKM 850.7), urinary bladder (RPKM 497.1) and 11 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COL1A1 in Genome Data Viewer
    Location:
    17q21.33
    Exon count:
    51
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (50184101..50201631, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51051162..51068680, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (48261462..48278992, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904025 Neighboring gene uncharacterized LOC105371818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8687 Neighboring gene Sharpr-MPRA regulatory region 13843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48240960-48241460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48252214-48252815 Neighboring gene sarcoglycan alpha Neighboring gene Sharpr-MPRA regulatory region 9980 Neighboring gene H1.9 linker histone, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48259283-48260178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48261754-48262744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48266067-48266622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48266623-48267176 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:48273702-48274901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48283085-48283586 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48287195-48287760 Neighboring gene long intergenic non-protein coding RNA 1969 Neighboring gene Sharpr-MPRA regulatory region 1443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12380 Neighboring gene SUMO2 pseudogene 7

    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
    Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1
    MedGen: C5436842 OMIM: 619115 GeneReviews: Not available
    Compare labs
    Ehlers-Danlos syndrome, arthrochalasis type
    MedGen: C4551623 OMIM: 130060 GeneReviews: Not available
    Compare labs
    Infantile cortical hyperostosis
    MedGen: C0020497 OMIM: 114000 GeneReviews: Caffey Disease
    Compare labs
    Osteogenesis imperfecta Compare labs
    Osteogenesis imperfecta type I Compare labs
    Osteogenesis imperfecta type III Compare labs
    Osteogenesis imperfecta with normal sclerae, dominant form Compare labs
    Osteogenesis imperfecta, recessive perinatal lethal Compare labs
    Osteoporosis
    MedGen: C0029456 OMIM: 166710 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2012-08-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2012-08-23)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.
    EBI GWAS Catalog
    Genetic association with overall survival of taxane-treated lung cancer patients - A genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 X4-tropic gp120 upregulates alpha-SMA (ACTA2) and collagen I alpha 1 expression via the ERK1/2 pathway in a CXCR4-dependent manner in activated human hepatic stellate cells PubMed
    Tat tat HIV-1 Tat, through its basic domain (amino acids 46-60), inhibits the adhesion of collagen I to the neuroblastoma cell line GI-CA-N, suggesting a role for Tat in the neurologic dysfunction and destruction of the CNS observed in infants infected with HIV-1 PubMed
    tat HIV-1 Tat upregulates the steady-state RNA levels for fibronectin and types I and III collagen in glioblastoma cells and salivary gland cell lines PubMed
    Vpu vpu HIV-1 Vpu-expressing U937 monocytes coculture with LX2 stellate cells to upregulate expression of profibrogenic markers COL-1, PCT, SMA-1, VEGF, and MMP2, which is inhibited by MIF treatment PubMed
    matrix gag Treatment of human stellate cells with HIV-1 MA upregulates the expression of CXCR2, syndecan-2, collagen-I, alpha-SMA, vimentin, and endothelin-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in blood vessel development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in blood vessel development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in bone trabecula formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage development involved in endochondral bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to amino acid stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to epidermal growth factor stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to fibroblast growth factor stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to fluoride IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to glucose stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to mechanical stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to retinoic acid IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to transforming growth factor beta stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to tumor necrosis factor IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to vitamin E IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in collagen biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in collagen fibril organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in collagen-activated tyrosine kinase receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endochondral ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in face morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intramembranous ossification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell-substrate adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ossification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of epithelial to mesenchymal transition IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein localization to nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to cAMP IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to estradiol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hydrogen peroxide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hyperoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to insulin IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to mechanical stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to steroid hormone IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in skin development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skin morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in tooth mineralization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in visual perception IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    collagen alpha-1(I) chain
    Names
    alpha-1 type I collagen
    alpha1(I) procollagen
    collagen alpha 1 chain type I
    collagen alpha-1(I) chain preproprotein
    collagen of skin, tendon and bone, alpha-1 chain
    collagen, type I, alpha 1
    pro-alpha-1 collagen type 1
    type I proalpha 1
    type I procollagen alpha 1 chain

    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_007400.1 RefSeqGene

      Range
      5001..22544
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1

    mRNA and Protein(s)

    1. NM_000088.4NP_000079.2  collagen alpha-1(I) chain preproprotein

      See identical proteins and their annotated locations for NP_000079.2

      Status: REVIEWED

      Source sequence(s)
      AB209597, AC015909
      Consensus CDS
      CCDS11561.1
      UniProtKB/Swiss-Prot
      O76045, P02452, P78441, Q13896, Q13902, Q13903, Q14037, Q14992, Q15176, Q15201, Q16050, Q59F64, Q7KZ30, Q7KZ34, Q8IVI5, Q8N473, Q9UML6, Q9UMM7
      Related
      ENSP00000225964.6, ENST00000225964.10
      Conserved Domains (5) summary
      PRK07764
      Location:449640
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      PRK12678
      Location:9081111
      PRK12678; transcription termination factor Rho; Provisional
      pfam00093
      Location:4095
      VWC; von Willebrand factor type C domain
      pfam01391
      Location:239295
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:12271463
      COLFI; Fibrillar collagen C-terminal domain

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      50184101..50201631 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005257059.5XP_005257116.2  collagen alpha-1(I) chain isoform X3

      Conserved Domains (3) summary
      pfam01391
      Location:236295
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00093
      Location:4095
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:9241157
      COLFI; Fibrillar collagen C-terminal domain
    2. XM_011524341.2XP_011522643.1  collagen alpha-1(I) chain isoform X1

      See identical proteins and their annotated locations for XP_011522643.1

      Conserved Domains (3) summary
      pfam01391
      Location:236295
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00093
      Location:4095
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:11641397
      COLFI; Fibrillar collagen C-terminal domain
    3. XM_005257058.5XP_005257115.2  collagen alpha-1(I) chain isoform X2

      See identical proteins and their annotated locations for XP_005257115.2

      Conserved Domains (3) summary
      pfam01391
      Location:236295
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00093
      Location:4095
      VWC; von Willebrand factor type C domain
      pfam01410
      Location:11401373
      COLFI; Fibrillar collagen C-terminal domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      51051162..51068680 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315083.1XP_054171058.1  collagen alpha-1(I) chain isoform X3

    2. XM_054315081.1XP_054171056.1  collagen alpha-1(I) chain isoform X1

    3. XM_054315082.1XP_054171057.1  collagen alpha-1(I) chain isoform X2