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

Gene ID: 1300, updated on 27-Nov-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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See COL10A1 in Genome Data Viewer
Location:
6q22.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116118909..116217144, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117302889..117401128, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116440072..116538307, 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. COL10A1 expression is elevated in diverse solid tumor types and is associated with tumor vasculature. Chapman KB, et al. Future Oncol, 2012 Aug. PMID 22894674
  2. A type X collagen mutation causes Schmid metaphyseal chondrodysplasia. Warman ML, et al. Nat Genet, 1993 Sep. PMID 8220429
  3. Schmid Type Metaphyseal Chondrodysplasia with a Novel COL10A1 Mutation. Goyal M, et al. Indian J Pediatr, 2019 Feb. PMID 30209734
  4. Amino acid substitutions of conserved residues in the carboxyl-terminal domain of the alpha 1(X) chain of type X collagen occur in two unrelated families with metaphyseal chondrodysplasia type Schmid. Wallis GA, et al. Am J Hum Genet, 1994 Feb. PMID 8304336, Free PMC Article
  5. Autosomal recessive chondrodysplasia with severe short stature caused by a biallelic COL10A1 variant. Ain NU, et al. J Med Genet, 2018 Jun. PMID 28830906

See all (99) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Oncogenic mechanisms of COL10A1 in cancer and clinical challenges (Review).
    Title: Oncogenic mechanisms of COL10A1 in cancer and clinical challenges (Review).
  2. METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts.
    Title: METTL16 Promotes Stability of SYNPO2L mRNA and leading to Cancer Cell Lung Metastasis by Secretion of COL10A1 and attract the Cancer-Associated Fibroblasts.
  3. LncRNA HAGLROS promotes breast cancer evolution through miR-135b-3p/COL10A1 axis and exosome-mediated macrophage M2 polarization.
    Title: LncRNA HAGLROS promotes breast cancer evolution through miR-135b-3p/COL10A1 axis and exosome-mediated macrophage M2 polarization.
  4. Upregulation of collagen type X alpha 1 promotes the progress of triple-negative breast cancer via Wnt/beta-catenin signaling.
    Title: Upregulation of collagen type X alpha 1 promotes the progress of triple-negative breast cancer via Wnt/β-catenin signaling.
  5. 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.
  6. COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma.
    Title: COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (57)

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
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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)

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_2024_08

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

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