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

Gene ID: 1300, updated on 3-Oct-2020

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
109.20200815 current GRCh38.p13 (GCF_000001405.39) 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 pseudogene 3 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
Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration.
GeneReviews: Not available
Metaphyseal chondrodysplasia, Schmid type Compare labs
Seven new loci associated with age-related macular degeneration.
GeneReviews: Not available

Pathways from PubChem

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 
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
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
    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
    Q03692
    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)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 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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