Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL10A1 Gene

Aliases for COL10A1 Gene

  • Collagen Type X Alpha 1 Chain 2 3 5
  • Schmid Metaphyseal Chondrodysplasia 2 3
  • Collagen, Type X, Alpha 1 2 3
  • Collagen X, Alpha-1 Polypeptide 3
  • Collagen Alpha-1(X) Chain 3

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 ERK Signaling and Collagen chain trimerization. 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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for COL10A1 Gene

Promoters and enhancers for COL10A1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J116217 Promoter/Enhancer 1.1 EPDnew ENCODE 650.7 +1.0 976 0.2 CTCF ZNF3 PKNOX1 ZNF654 TRIM22 CEBPB CEBPG ZNF384 RAD21 ATF4 COL10A1 GC06M116148 NT5DC1
GH06J116158 Promoter 0.5 EPDnew 650.2 +59.4 59394 0.1 COL10A1 GC06M116178 NIP7P3 GC06M116148 NT5DC1
GH06J116126 Promoter 0.5 EPDnew 650.2 +92.0 92017 0.1 COL10A1 NIP7P3 NT5DC1
GH06J116098 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 11.1 +117.5 117519 4.7 HDGF PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B NT5DC1 FRK KPNA5 COL10A1 ZUP1 TSPYL4 GC06M116078
GH06J116228 Enhancer 1.1 FANTOM5 Ensembl ENCODE 0.4 -11.3 -11316 1.1 MXI1 PKNOX1 ATF1 RFX1 MAX BMI1 RFX5 ZNF217 SP1 MTA1 DSE TSPYL4 KPNA5 TSPYL1 GC06P116234 GC06P116233 PIR35709 COL10A1 NT5DC1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COL10A1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the COL10A1 gene promoter:
  • ARP-1
  • TBP
  • NF-kappaB2
  • NF-kappaB
  • NF-kappaB1
  • ISGF-3
  • Sox9
  • STAT5A
  • AML1a

Genomic Locations for COL10A1 Gene

Genomic Locations for COL10A1 Gene
99,261 bases
Minus strand
39,826 bases
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:
    Recommended name:
    Collagen alpha-1(X) chain
    Protein Accession:
    Secondary Accessions:
    • A1L4P2

    Protein attributes for COL10A1 Gene

    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

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

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted secreted proteins

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

UniProtKB/Swiss-Prot Function:
Type X collagen is a product of hypertrophic chondrocytes and has been localized to presumptive mineralization zones of hyaline cartilage.
GENATLAS Biochemistry:
collagen,type X,alpha 1,short chain,expressed by chondrocytes in the hypertrophic region of the growth plate cartilage

Phenotypes From GWAS Catalog for COL10A1 Gene

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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL10A1

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

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COL10A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005581 collagen trimer TAS,IEA --
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:0030198 extracellular matrix organization 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

mRNA/cDNA for COL10A1 Gene

Unigene Clusters for COL10A1 Gene

Collagen, type X, alpha 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COL10A1

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

No ASD Table

Relevant External Links for COL10A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

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 and MOPED for COL10A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL10A1 Gene:


SOURCE GeneReport for Unigene cluster for COL10A1 Gene:


Evidence on tissue expression from TISSUES for COL10A1 Gene

  • Bone(2.4)

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

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • chin
  • ear
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • pelvis
  • 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
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with COL10A1: view

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
(Pan troglodytes)
Mammalia COL10A1 34 33
  • 99.22 (n)
(Bos Taurus)
Mammalia COL10A1 34 33
  • 86.94 (n)
(Canis familiaris)
Mammalia COL10A1 34 33
  • 86.1 (n)
(Monodelphis domestica)
Mammalia COL10A1 34
  • 86 (a)
(Mus musculus)
Mammalia Col10a1 16 34 33
  • 85.69 (n)
(Ornithorhynchus anatinus)
Mammalia COL10A1 34
  • 79 (a)
(Gallus gallus)
Aves COL10A1 34
  • 74 (a)
LOC100858979 33
  • 70.93 (n)
(Anolis carolinensis)
Reptilia COL10A1 34
  • 74 (a)
(Danio rerio)
Actinopterygii col10a1a 33
  • 59.22 (n)
col10a1 34
  • 55 (a)
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

Gene Tree for COL10A1 (if available)
Gene Tree for COL10A1 (if available)
Evolutionary constrained regions (ECRs) for COL10A1: view image

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 Variation AA Info Type
rs1007346045 uncertain-significance, Metaphyseal chondrodysplasia 116,120,696(-) G/A/C coding_sequence_variant, missense_variant
rs1059277 benign, Metaphyseal chondrodysplasia 116,119,047(-) C/T 3_prime_UTR_variant
rs1064583 benign, not specified, Metaphyseal chondrodysplasia 116,125,413(-) A/G coding_sequence_variant, missense_variant
rs111033543 pathogenic, Metaphyseal chondrodysplasia, Schmid type 116,120,232(-) G/C coding_sequence_variant, stop_gained
rs111033544 pathogenic, Metaphyseal chondrodysplasia, Schmid type, Schmid type metaphyseal chondrodysplasia (SMCD) [MIM:156500] 116,120,324(-) A/C coding_sequence_variant, missense_variant

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)

Additional Variant Information for COL10A1 Gene

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

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: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • 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.

Additional Disease Information for COL10A1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 BR (FEBS letters 1991) 2 3 4 22 58
  2. Mutations of COL10A1 in Schmid metaphyseal chondrodysplasia. (PMID: 15880705) Bateman JF … Savarirayan R (Human mutation 2005) 3 4 22 58
  3. Mutation of the type X collagen gene (COL10A1) causes spondylometaphyseal dysplasia. (PMID: 9837818) Ikegawa S … Nakamura Y (American journal of human genetics 1998) 3 4 22 58
  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 (Journal of human genetics 1998) 3 4 22 58
  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 (Human mutation 1997) 3 4 22 58

Products for COL10A1 Gene

Sources for COL10A1 Gene

Loading form....