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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

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