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Aliases for COL10A1 Gene

Aliases for COL10A1 Gene

  • Collagen Type X Alpha 1 2 3
  • Collagen, Type X, Alpha 1 2 5
  • Schmid Metaphyseal Chondrodysplasia 2

External Ids for COL10A1 Gene

Previous GeneCards Identifiers for COL10A1 Gene

  • GC06M116275
  • GC06M116462
  • GC06M116485
  • GC06M116546
  • GC06M116440
  • GC06M114020

Summaries for COL10A1 Gene

Entrez Gene Summary for COL10A1 Gene

  • 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]

GeneCards Summary for COL10A1 Gene

COL10A1 (Collagen Type X Alpha 1) is a Protein Coding gene. Diseases associated with COL10A1 include metaphyseal chondrodysplasia, schmid type and cartilage-hair hypoplasia. Among its related pathways are Protein digestion and absorption and Collagen biosynthesis and modifying enzymes. An important paralog of this gene is COL8A1.

UniProtKB/Swiss-Prot for COL10A1 Gene

  • Type X collagen is a product of hypertrophic chondrocytes and has been localized to presumptive mineralization zones of hyaline cartilage.

Gene Wiki entry for COL10A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL10A1 Gene

Genomics for COL10A1 Gene

Regulatory Elements for COL10A1 Gene

Enhancers for COL10A1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around COL10A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL10A1 Gene

Chromosome:
6
Start:
116,118,909 bp from pter
End:
116,218,169 bp from pter
Size:
99,261 bases
Orientation:
Minus strand

Genomic View for COL10A1 Gene

Genes around COL10A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL10A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL10A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL10A1 Gene

Proteins for COL10A1 Gene

  • Protein details for COL10A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q03692-COAA1_HUMAN
    Recommended name:
    Collagen alpha-1(X) chain
    Protein Accession:
    Q03692
    Secondary Accessions:
    • A1L4P2

    Protein attributes for COL10A1 Gene

    Size:
    680 amino acids
    Molecular mass:
    66158 Da
    Quaternary structure:
    • Homotrimer.

    Three dimensional structures from OCA and Proteopedia for COL10A1 Gene

neXtProt entry for COL10A1 Gene

Proteomics data for COL10A1 Gene at MOPED

Post-translational modifications for COL10A1 Gene

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for COL10A1 Gene

No data available for DME Specific Peptides for COL10A1 Gene

Domains & Families for COL10A1 Gene

Gene Families for COL10A1 Gene

Suggested Antigen Peptide Sequences for COL10A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q03692

UniProtKB/Swiss-Prot:

COAA1_HUMAN :
  • Contains 1 C1q domain.
Domain:
  • Contains 1 C1q domain.
genes like me logo Genes that share domains with COL10A1: view

Function for COL10A1 Gene

Molecular function for COL10A1 Gene

GENATLAS Biochemistry:
collagen,type X,alpha 1,short chain,expressed by chondrocytes in the hypertrophic region of the growth plate cartilage
UniProtKB/Swiss-Prot Function:
Type X collagen is a product of hypertrophic chondrocytes and has been localized to presumptive mineralization zones of hyaline cartilage.
genes like me logo Genes that share phenotypes with COL10A1: view

Human Phenotype Ontology for COL10A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for COL10A1 Gene

MGI Knock Outs for COL10A1:

Animal Model Products

CRISPR Products

miRNA for COL10A1 Gene

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for COL10A1 Gene

Localization for COL10A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL10A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL10A1 Gene COMPARTMENTS Subcellular localization image for COL10A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
lysosome 1
nucleus 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for COL10A1 Gene

Pathways & Interactions for COL10A1 Gene

genes like me logo Genes that share pathways with COL10A1: view

Gene Ontology (GO) - Biological Process for COL10A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0022617 extracellular matrix disassembly TAS --
GO:0030574 collagen catabolic process TAS --
genes like me logo Genes that share ontologies with COL10A1: view

No data available for SIGNOR curated interactions for COL10A1 Gene

Drugs & Compounds for COL10A1 Gene

No Compound Related Data Available

Transcripts for COL10A1 Gene

Unigene Clusters for COL10A1 Gene

Collagen, type X, alpha 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for COL10A1 Gene

No ASD Table

Relevant External Links for COL10A1 Gene

GeneLoc Exon Structure for
COL10A1
ECgene alternative splicing isoforms for
COL10A1

Expression for COL10A1 Gene

mRNA expression in normal human tissues for COL10A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for COL10A1 Gene

This gene is overexpressed in Breast (34.0), Pancreas (20.6), and Bone marrow mesenchymal stem cell (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL10A1 Gene



SOURCE GeneReport for Unigene cluster for COL10A1 Gene Hs.520339

genes like me logo Genes that share expression patterns with COL10A1: view

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for COL10A1 Gene

Orthologs for COL10A1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for COL10A1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL10A1 35
  • 86.94 (n)
  • 86.65 (a)
COL10A1 36
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL10A1 35
  • 86.1 (n)
  • 87.54 (a)
COL10A1 36
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col10a1 35
  • 85.69 (n)
  • 87.35 (a)
Col10a1 16
Col10a1 36
  • 87 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL10A1 35
  • 99.22 (n)
  • 98.53 (a)
COL10A1 36
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL10A1 36
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL10A1 36
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC100858979 35
  • 70.93 (n)
  • 74.89 (a)
COL10A1 36
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL10A1 36
  • 74 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii col10a1a 35
  • 59.22 (n)
  • 56.43 (a)
col10a1 36
  • 55 (a)
OneToOne
Species with no ortholog for COL10A1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for COL10A1 Gene

ENSEMBL:
Gene Tree for COL10A1 (if available)
TreeFam:
Gene Tree for COL10A1 (if available)

Paralogs for COL10A1 Gene

(10) SIMAP similar genes for COL10A1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with COL10A1: view

Variants for COL10A1 Gene

Sequence variations from dbSNP and Humsavar for COL10A1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
VAR_001838 Schmid type metaphyseal chondrodysplasia (SMCD)
VAR_001839 Schmid type metaphyseal chondrodysplasia (SMCD)
VAR_001840 -
VAR_001841 Schmid type metaphyseal chondrodysplasia (SMCD)
VAR_001842 Schmid type metaphyseal chondrodysplasia (SMCD)

Structural Variations from Database of Genomic Variants (DGV) for COL10A1 Gene

Variant ID Type Subtype PubMed ID
nsv523972 CNV Gain 19592680

Variation tolerance for COL10A1 Gene

Residual Variation Intolerance Score: 72.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.97; 94.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL10A1 Gene

HapMap Linkage Disequilibrium report
COL10A1
Human Gene Mutation Database (HGMD)
COL10A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL10A1 Gene

Disorders for COL10A1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for COL10A1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
metaphyseal chondrodysplasia, schmid type
  • smcd
cartilage-hair hypoplasia
  • mckusick type metaphyseal chondrodysplasia
cartilage disease
  • cartilage disorder
subepithelial mucinous corneal dystrophy
  • smcd
smed strudwick type
  • spondyloepimetaphyseal dysplasia, strudwick type
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

COAA1_HUMAN
  • Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500]: Dominantly inherited disorder of the osseous skeleton. The cardinal features of the phenotype are mild short stature, coxa vara and a waddling gait. Radiography usually shows sclerosis of the ribs, flaring of the metaphyses, and a wide irregular growth plate, especially of the knees. A variant form of SMCD is spondylometaphyseal dysplasia Japanese type. It is characterized by spinal involvement comprising mild platyspondyly, vertebral body abnormalities, and end-plate irregularity. {ECO:0000269 PubMed:15880705, ECO:0000269 PubMed:7607655, ECO:0000269 PubMed:7876225, ECO:0000269 PubMed:8004099, ECO:0000269 PubMed:8304336, ECO:0000269 PubMed:8782043, ECO:0000269 PubMed:9067753, ECO:0000269 PubMed:9852679}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL10A1

Genetic Association Database (GAD)
COL10A1
Human Genome Epidemiology (HuGE) Navigator
COL10A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL10A1
genes like me logo Genes that share disorders with COL10A1: view

No data available for Genatlas for COL10A1 Gene

Publications for COL10A1 Gene

  1. Cloning of human alpha 1(X) collagen DNA and localization of the COL10A1 gene to the q21-q22 region of human chromosome 6. (PMID: 2037056) Apte S. … Olsen B.R. (FEBS Lett. 1991) 2 3 4 23 67
  2. Identification of the core element responsive to runt-related transcription factor 2 in the promoter of human type X collagen gene. (PMID: 19116917) Higashikawa A. … Kawaguchi H. (Arthritis Rheum. 2009) 3 23
  3. Expression of cartilage-specific markers in calcified and non-calcified atherosclerotic lesions. (PMID: 17335825) Aigner T. … Amann K. (Atherosclerosis 2008) 3 23
  4. Correlation of COL10A1 induction during chondrogenesis of mesenchymal stem cells with demethylation of two CpG sites in the COL10A1 promoter. (PMID: 18759285) Zimmermann P. … Richter W. (Arthritis Rheum. 2008) 3 23
  5. A multiplex family with possible metaphyseal Spahr-type dysplasia and exclusion of RMRP and COL10A1 as candidate genes. (PMID: 18553549) MAcgarbanAc A. … Ghanem I. (Am. J. Med. Genet. A 2008) 3 23

Products for COL10A1 Gene

Sources for COL10A1 Gene

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