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    COL10A1 collagen type X alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1300, updated on 17-Jun-2024

    Summary

    Official Symbol
    COL10A1provided by HGNC
    Official Full Name
    collagen type X alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2185
    See related
    Ensembl:ENSG00000123500 MIM:120110; AllianceGenome:HGNC:2185
    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
    Summary
    This gene encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X collagen is a homotrimer. Mutations in this gene are associated with Schmid type metaphyseal chondrodysplasia (SMCD) and Japanese type spondylometaphyseal dysplasia (SMD). [provided by RefSeq, Jul 2008]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
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    Genomic context

    See COL10A1 in Genome Data Viewer
    Location:
    6q22.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116118909..116217144, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117302889..117401128, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116440072..116447295, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901385 Neighboring gene NANOG hESC enhancer GRCh37_chr6:116235207-116235708 Neighboring gene fyn related Src family tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24976 Neighboring gene triosephosphate isomerase 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24978 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24979 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:116412309-116412554 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116421676-116422198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:116422199-116422719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24980 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88050 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88070 Neighboring gene Sharpr-MPRA regulatory region 2872 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_88113 Neighboring gene 5'-nucleotidase domain containing 1 Neighboring gene MPRA-validated peak6050 silencer Neighboring gene NIP7 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24982 Neighboring gene ribosomal protein S5 pseudogene Neighboring gene TSPY like 4 Neighboring gene RPS5 pseudogene 1 Neighboring gene dermatan sulfate epimerase

    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
    Metaphyseal chondrodysplasia, Schmid type Compare labs

    EBI GWAS Catalog

    Description
    Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration.
    EBI GWAS Catalog
    Seven new loci associated with age-related macular degeneration.
    EBI GWAS Catalog

    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 extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal system development TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of collagen trimer TAS
    Traceable Author Statement
    more info
    PubMed 
    part_of collagen type X trimer IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in collagen-containing extracellular matrix EXP
    Inferred from Experiment
    more info
    PubMed 
    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
     

    General protein information

    Preferred Names
    collagen alpha-1(X) chain
    Names
    Schmid metaphyseal chondrodysplasia
    collagen X, alpha-1 polypeptide
    collagen, type X, alpha 1

    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_008032.1 RefSeqGene

      Range
      5002..12225
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000493.4NP_000484.2  collagen alpha-1(X) chain precursor

      See identical proteins and their annotated locations for NP_000484.2

      Status: REVIEWED

      Source sequence(s)
      AL121963, BI521533, CA447328
      Consensus CDS
      CCDS5105.1
      UniProtKB/Swiss-Prot
      A1L4P2, Q03692
      UniProtKB/TrEMBL
      A0A650AXN9
      Related
      ENSP00000498802.1, ENST00000651968.1
      Conserved Domains (2) summary
      smart00110
      Location:545680
      C1Q; Complement component C1q domain
      pfam01391
      Location:326383
      Collagen; Collagen triple helix repeat (20 copies)
    2. NM_001424106.1NP_001411035.1  collagen alpha-1(X) chain precursor

      Status: REVIEWED

      Source sequence(s)
      AL121963
      UniProtKB/Swiss-Prot
      A1L4P2, Q03692
      UniProtKB/TrEMBL
      A0A650AXN9
    3. NM_001424107.1NP_001411036.1  collagen alpha-1(X) chain precursor

      Status: REVIEWED

      Source sequence(s)
      AL050331, AL121963
      UniProtKB/Swiss-Prot
      A1L4P2, Q03692
      UniProtKB/TrEMBL
      A0A650AXN9

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      116118909..116217144 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535433.4XP_011533735.1  collagen alpha-1(X) chain isoform X1

      See identical proteins and their annotated locations for XP_011533735.1

      UniProtKB/Swiss-Prot
      A1L4P2, Q03692
      UniProtKB/TrEMBL
      A0A650AXN9
      Related
      ENSP00000327368.4, ENST00000327673.4
      Conserved Domains (2) summary
      smart00110
      Location:545680
      C1Q; Complement component C1q domain
      pfam01391
      Location:326383
      Collagen; Collagen triple helix repeat (20 copies)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      117302889..117401128 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354221.1XP_054210196.1  collagen alpha-1(X) chain isoform X1

      UniProtKB/Swiss-Prot
      A1L4P2, Q03692
      UniProtKB/TrEMBL
      A0A650AXN9