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

Gene ID: 1300, updated on 7-Dec-2018

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
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

Genomic context

See COL10A1 in Genome Data Viewer
Location:
6q22.1
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (116118909..116219937, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116440085..116447296, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2534 Neighboring gene fyn related Src family tyrosine kinase Neighboring gene triosephosphate isomerase 1 pseudogene 3 Neighboring gene 5'-nucleotidase domain containing 1 Neighboring gene NIP7, nucleolar pre-rRNA processing protein pseudogene 3 Neighboring gene ribosomal protein S5 pseudogene Neighboring gene TSPY like 4 Neighboring gene ribosomal protein S5 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 FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Metaphyseal chondrodysplasia, Schmid type
MedGen: C0265289 OMIM: 156500 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
    Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
  • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
    Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
    Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Senescence and Autophagy in Cancer, organism-specific biosystem (from WikiPathways)
    Senescence and Autophagy in Cancer, organism-specific biosystemSenescense and Autophagy Pathways in Cancer

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength HDA PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
skeletal system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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)

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
    5001..12212
    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
    Q03692
    Related
    ENSP00000243222.4, ENST00000243222.8
    Conserved Domains (2) summary
    smart00110
    Location:545680
    C1Q; Complement component C1q domain
    pfam01391
    Location:326383
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    116118909..116219937 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535432.3XP_011533734.1  collagen alpha-1(X) chain isoform X1

    See identical proteins and their annotated locations for XP_011533734.1

    UniProtKB/Swiss-Prot
    Q03692
    Conserved Domains (2) summary
    smart00110
    Location:545680
    C1Q; Complement component C1q domain
    pfam01391
    Location:326383
    Collagen; Collagen triple helix repeat (20 copies)
  2. XM_011535433.3XP_011533735.1  collagen alpha-1(X) chain isoform X1

    See identical proteins and their annotated locations for XP_011533735.1

    UniProtKB/Swiss-Prot
    Q03692
    Conserved Domains (2) summary
    smart00110
    Location:545680
    C1Q; Complement component C1q domain
    pfam01391
    Location:326383
    Collagen; Collagen triple helix repeat (20 copies)
  3. XM_006715333.3XP_006715396.1  collagen alpha-1(X) chain isoform X1

    See identical proteins and their annotated locations for XP_006715396.1

    UniProtKB/Swiss-Prot
    Q03692
    Conserved Domains (2) summary
    smart00110
    Location:545680
    C1Q; Complement component C1q domain
    pfam01391
    Location:326383
    Collagen; Collagen triple helix repeat (20 copies)
  4. XM_017010248.1XP_016865737.1  collagen alpha-1(X) chain isoform X1

    UniProtKB/Swiss-Prot
    Q03692
    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)
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