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

    Gene ID: 1300, updated on 5-Mar-2024

    Summary

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    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
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    Genomic context

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    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

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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-Based Analysis: Noncoding RNA-Mediated COL10A1 Is Associated with Poor Prognosis and Immune Cell Infiltration in Pancreatic Cancer. Liu Q, et al. J Healthc Eng, 2022. PMID 36105715, Free PMC Article
    2. High COL10A1 expression potentially contributes to poor outcomes in gastric cancer with the help of LEF1 and Wnt2. Zhang M, et al. J Clin Lab Anal, 2022 Sep. PMID 35929139, Free PMC Article
    3. Identification of a novel COL10A1: c.1952 G>T variant in a family with Schmid metaphyseal chondrodysplasia and development of a noninvasive prenatal testing method. Ye Y, et al. Mol Genet Genomic Med, 2021 Oct. PMID 34423584, Free PMC Article
    4. Analysis of Collagen type X alpha 1 (COL10A1) expression and prognostic significance in gastric cancer based on bioinformatics. Chen S, et al. Bioengineered, 2021 Dec. PMID 33371777, Free PMC Article
    5. Genome-Scale Analysis Identifies Novel Transcript-Variants in Esophageal Adenocarcinoma. Purkayastha BPD, et al. Cell Mol Gastroenterol Hepatol, 2020. PMID 32344180, Free PMC Article

    See all (90) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Experimental validation and pan-cancer analysis identified COL10A1 as a novel oncogene and potential therapeutic target in prostate cancer.
      Title: Experimental validation and pan-cancer analysis identified COL10A1 as a novel oncogene and potential therapeutic target in prostate cancer.
    2. COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma.
      Title: COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma.
    3. COL10A1 is a potential immunotherapy biomarker associated with immune infiltration and deficient mismatch repair in colon cancer.
      Title: COL10A1 is a potential immunotherapy biomarker associated with immune infiltration and deficient mismatch repair in colon cancer.
    4. Natural history and genetic spectrum of the Turkish metaphyseal dysplasia cohort, including rare types caused by biallelic COL10A1, COL2A1, and LBR variants.
      Title: Natural history and genetic spectrum of the Turkish metaphyseal dysplasia cohort, including rare types caused by biallelic COL10A1, COL2A1, and LBR variants.
    5. Bioinformatics-Based Analysis: Noncoding RNA-Mediated COL10A1 Is Associated with Poor Prognosis and Immune Cell Infiltration in Pancreatic Cancer.
      Title: Bioinformatics-Based Analysis: Noncoding RNA-Mediated COL10A1 Is Associated with Poor Prognosis and Immune Cell Infiltration in Pancreatic Cancer.
    6. High COL10A1 expression potentially contributes to poor outcomes in gastric cancer with the help of LEF1 and Wnt2.
      Title: High COL10A1 expression potentially contributes to poor outcomes in gastric cancer with the help of LEF1 and Wnt2.
    7. VSNL1 Promotes Cell Proliferation, Migration, and Invasion in Colorectal Cancer by Binding with COL10A1.
      Title: VSNL1 Promotes Cell Proliferation, Migration, and Invasion in Colorectal Cancer by Binding with COL10A1.
    8. Identification of a novel COL10A1: c.1952 G>T variant in a family with Schmid metaphyseal chondrodysplasia and development of a noninvasive prenatal testing method.
      Title: Identification of a novel COL10A1: c.1952 G>T variant in a family with Schmid metaphyseal chondrodysplasia and development of a noninvasive prenatal testing method.
    9. COL10A1 is a novel factor in the development of choroidal neovascularization.
      Title: COL10A1 is a novel factor in the development of choroidal neovascularization.
    10. Differentiation of Hypertrophic Chondrocytes from Human iPSCs for the In Vitro Modeling of Chondrodysplasias.
      Title: Differentiation of Hypertrophic Chondrocytes from Human iPSCs for the In Vitro Modeling of Chondrodysplasias.
    Submit: New GeneRIF Correction See all GeneRIFs (53)

    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
    Metaphyseal chondrodysplasia, Schmid type
    MedGen: C0265289 OMIM: 156500 GeneReviews: Schmid Metaphyseal Chondrodysplasia
    		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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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

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    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)

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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_008032.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_000493.4 → NP_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:545 → 680
      C1Q; Complement component C1q domain
      pfam01391
      Location:326 → 383
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_001424106.1 → NP_001411035.1  collagen alpha-1(X) chain precursor

      Status: REVIEWED

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

    3. NM_001424107.1 → NP_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_011535433.4 → XP_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:545 → 680
      C1Q; Complement component C1q domain
      pfam01391
      Location:326 → 383
      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_054354221.1 → XP_054210196.1  collagen alpha-1(X) chain isoform X1

      UniProtKB/Swiss-Prot
      A1L4P2, Q03692
      UniProtKB/TrEMBL
      A0A650AXN9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q03692.2 GenPept UniProtKB/Swiss-Prot:Q03692

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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