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Aliases for COL10A1 Gene

Aliases for COL10A1 Gene

  • Collagen Type X Alpha 1 Chain 2 3 5
  • Schmid Metaphyseal Chondrodysplasia 2
  • Collagen, Type X, Alpha 1 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 Chain) is a Protein Coding gene. Diseases associated with COL10A1 include Metaphyseal Chondrodysplasia, Schmid Type and Cartilage Disease. Among its related pathways are Collagen chain trimerization and Phospholipase-C Pathway. 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 CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G116098 1.4 Ensembl ENCODE 11.1 +117.5 117519 4.7 HDGF HNRNPUL1 PKNOX1 CREB3L1 ZFP64 WRNIP1 ARID4B SIN3A FEZF1 DMAP1 KPNA5 NT5DC1 COL10A1 TSPYL4 FRK GC06M116078
GH06G116228 1.5 FANTOM5 Ensembl ENCODE 0.4 -11.3 -11316 1.1 ELF3 PKNOX1 FOXA2 ATF1 MLX SIN3A ARID4B BMI1 THRB YY1 DSE TSPYL4 KPNA5 TSPYL1 PIR35709 GC06P116234 GC06P116233 COL10A1
GH06G116217 0.7 ENCODE 0.7 +1.0 977 0.2 CTCF PKNOX1 ZNF654 ZNF3 TRIM22 CEBPB ZNF384 CEBPG RAD21 PRDM6 COL10A1 GC06M116148
GH06G116210 0.8 ENCODE 0.4 +7.2 7232 0.9 TBP CTCF ARNT ZNF2 RAD21 FOXK2 ZNF366 SCRT2 SMC3 PRDM10 DSE TSPYL4 COL10A1 GC06M116148
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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

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

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

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

No data available for UniProtKB/Swiss-Prot for COL10A1 Gene

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.

Gene Ontology (GO) - Molecular Function for COL10A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with COL10A1: view
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

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL10A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
nucleus 1
lysosome 1

Gene Ontology (GO) - Cellular Components for COL10A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA,TAS --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005938 cell cortex IEA --
genes like me logo Genes that share ontologies with COL10A1: view

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:0001501 skeletal system development TAS 8554571
GO:0001958 endochondral ossification IEA --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
GO:0051216 cartilage development IEA --
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:

CRISPR Products

Inhibitory RNA Products

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



NURSA nuclear receptor signaling pathways regulating expression of COL10A1 Gene:

COL10A1

SOURCE GeneReport for Unigene cluster for COL10A1 Gene:

Hs.520339

Evidence on tissue expression from TISSUES for COL10A1 Gene

  • Bone(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for COL10A1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • chin
  • ear
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with COL10A1: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt 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
chimpanzee
(Pan troglodytes)
Mammalia COL10A1 34 35
  • 99.22 (n)
cow
(Bos Taurus)
Mammalia COL10A1 34 35
  • 86.94 (n)
dog
(Canis familiaris)
Mammalia COL10A1 34 35
  • 86.1 (n)
oppossum
(Monodelphis domestica)
Mammalia COL10A1 35
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col10a1 34 16 35
  • 85.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COL10A1 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL10A1 35
  • 74 (a)
OneToOne
LOC100858979 34
  • 70.93 (n)
lizard
(Anolis carolinensis)
Reptilia COL10A1 35
  • 74 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii col10a1a 34
  • 59.22 (n)
col10a1 35
  • 55 (a)
OneToOne
Species where no ortholog for COL10A1 was found in the sources mined by GeneCards:
  • 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
rs111033544 Pathogenic, Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500] 116,120,324(-) TATAC(G/T)ATTTT intron-variant, reference, missense
rs111033545 Pathogenic, Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500] 116,120,275(-) AGGCC(C/T)GTATA intron-variant, reference, missense
rs111033546 Pathogenic, Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500] 116,120,345(-) TTACT(C/T)GTCAG intron-variant, reference, missense
rs111033549 Pathogenic, Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500] 116,120,165(-) AGGTG(C/T)GGCTC intron-variant, reference, missense
rs111033550 Pathogenic, Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500] 116,125,441(-) TTCAT(A/G)GAGTG intron-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
esv3576211 CNV gain 25503493
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

Human Gene Mutation Database (HGMD)
COL10A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL10A1

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

Disorders for COL10A1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
metaphyseal chondrodysplasia, schmid type
  • corneal dystrophy, subepithelial mucinous
cartilage disease
  • cartilage disorder
cartilage-hair hypoplasia
  • mckusick type metaphyseal chondrodysplasia
corneal dystrophy, subepithelial mucinous
  • subepithelial mucinous corneal dystrophy
pyle disease
  • metaphyseal dysplasia
- 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 22 64
  2. Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia. (PMID: 15880705) Bateman J.F. … Savarirayan R. (Hum. Mutat. 2005) 3 4 22 64
  3. Mutation of the type X collagen gene 'COL10A1' causes spondylometaphyseal dysplasia. (PMID: 9837818) Ikegawa S. … Nakamura Y. (Am. J. Hum. Genet. 1998) 3 4 22 64
  4. Novel missense mutation resulting in the substitution of tyrosine by cysteine at codon 597 of the type X collagen gene associated with Schmid metaphyseal chondrodysplasia. (PMID: 9852679) Sawai H. … Koyama K. (J. Hum. Genet. 1998) 3 4 22 64
  5. Mutations in the N-terminal globular domain of the type X collagen gene (COL10A1) in patients with schmid metaphyseal chondrodysplasia. (PMID: 9067753) Ikegawa S. … Nakamura Y. (Hum. Mutat. 1997) 3 4 22 64

Products for COL10A1 Gene

Sources for COL10A1 Gene

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