Tbio COL10A1 Collagen alpha-1(X) chain

Protein Summary

Description

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

Uniprot Accession IDs

• Q03692
• A1L4P2

Gene Name

• COL10A1

Ensembl ID

• ENST00000243222
• ENSP00000243222
• ENSG00000123500
• ENST00000327673
• ENSP00000327368

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
gene perturbation	0.7
small molecule perturbation	0.59
phenotype	0.54
biological term	0.53
cell line	0.52

Protein Classes

PANTHER Classes

Protein / Extracellular Matrix Protein / Extracellular Matrix Structural Protein / Collagen Alpha-1(x) Chain

DTO Classes

Protein / Extracellular Structure / Extracellular Matrix Structural Protein / Collagen Alpha-1(x) Chain

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 182.47   (req: < 5)

Gene RIFs: 29   (req: <= 3)

Antibodies: 125   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 182.47   (req: >= 5)

Gene RIFs: 29   (req: > 3)

Antibodies: 125   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 5

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Protein Sequence and Structure

Residue Counts

Protein Sequence

Find Targets by Sequence

Show Full Sequence

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Expression Data (0 Tissues)

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No expression data found

Related Tools

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (135)

Explore Interacting Targets

1 – 10 of 135

• See Interactions on String-DB

C1QL4

Tdark

Novelty:  0.37071722

p_int:  0.999586311

p_ni:  0.000413689

Score:  0.202

Data Source:  BioPlex,STRINGDB

C1QL1

Tdark

Novelty:  0.11689088

p_int:  0.999474253

p_ni:  0.000520165

p_wrong:  0.000005583

Score:  0.18

Data Source:  BioPlex,STRINGDB

TOMM34

Tbio

Novelty:  0.05433718

p_int:  0.990880095

p_ni:  0.009119905

Score:  0.188

Data Source:  BioPlex,STRINGDB

COLGALT2

Tbio

Family:  Enzyme

Novelty:  0.15981994

p_int:  0.938605623

p_ni:  0.061393753

p_wrong:  6.23e-7

Score:  0.929

Data Source:  BioPlex,STRINGDB

NUMB

Tbio

Novelty:  0.00211228

p_int:  0.935987305

p_ni:  0.064002708

p_wrong:  0.000009988

Score:  0.214

Data Source:  BioPlex,STRINGDB

COL4A2

Tbio

Novelty:  0.00782053

p_int:  0.905750056

p_ni:  0.094249318

p_wrong:  6.26e-7

Score:  0.961

Data Source:  BioPlex,STRINGDB

MPP1

Tbio

Novelty:  0.08674817

p_int:  0.862834343

p_ni:  0.135630803

p_wrong:  0.001534854

Score:  0.305

Data Source:  BioPlex,STRINGDB

COL11A1

Tbio

Novelty:  0.00594683

Score:  0.935

Data Source:  STRINGDB

COL2A1

Tbio

Novelty:  0.0011102

Score:  0.932

Data Source:  STRINGDB

COL1A1

Tbio

Novelty:  0.00063584

Score:  0.931

Data Source:  STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (37)

Reactome (5)

KEGG (1)

PathwayCommons (2)

WikiPathways (29)

Assembly of collagen fibrils and other multimeric structures (R-HSA-2022090)

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5

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Assembly of collagen fibrils and other multimeric structures	57 targets	R-HSA-2022090
Reactome	Collagen biosynthesis and modifying enzymes	67 targets	R-HSA-1650814
Reactome	Collagen chain trimerization	44 targets	R-HSA-8948216
Reactome	Collagen formation	90 targets	R-HSA-1474290
Reactome	Extracellular matrix organization	297 targets	R-HSA-1474244

Name	Explore in Pharos	Explore in Source
Assembly of collagen fibrils and other multimeric structures	57 targets	R-HSA-2022090
Collagen biosynthesis and modifying enzymes	67 targets	R-HSA-1650814
Collagen chain trimerization	44 targets	R-HSA-8948216
Collagen formation	90 targets	R-HSA-1474290
Extracellular matrix organization	297 targets	R-HSA-1474244

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (11)

Functions (3)

Components (6)

Processes (2)

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Items per page:

10

1 – 3 of 3

GO Term	Evidence	Assigned by
extracellular matrix structural constituent conferring tensile strength	Inferred from High Throughput Direct Assay (HDA)	BHF-UCL
extracellular matrix structural constituent	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

Disease Associations ()

No disease associations found

GWAS Traits (9)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 9

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
low density lipoprotein cholesterol measurement	EFO_0004611	3	3	3		83.1
total cholesterol measurement	EFO_0004574	3	3	3		69.4
refractive error measurement	EFO_0007814	2	2	1	6.5	64.2
Myopia	HP_0000545	2	1	0	3.8	58.4
age at onset	EFO_0004847	1	1	0	6.5	46.1

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 9

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
low density lipoprotein cholesterol measurement	EFO_0004611	3		83.1
total cholesterol measurement	EFO_0004574	3		69.4
refractive error measurement	EFO_0007814	1	6.5	64.2
Myopia	HP_0000545	0	3.8	58.4
age at onset	EFO_0004847	0	6.5	46.1

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Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Calcium
Collagen
Complete proteome
Disease mutation
Extracellular matrix
Hydroxylation
Metal-binding
Polymorphism
Reference proteome

GWAS Trait Find Similar Targets

No Header	No Header
adolescent idiopathic scoliosis
age at onset
age-related macular degeneration
C-reactive protein measurement
hematocrit
low density lipoprotein cholesterol measurement
Myopia
refractive error measurement
total cholesterol measurement

MGI Phenotype Find Similar Targets

No Header	No Header
behavior/neurological phenotype
cellular phenotype
craniofacial phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
hematopoietic system phenotype
immune system phenotype
limbs/digits/tail phenotype
mortality/aging
nervous system phenotype

IDG Resources

No IDG generated resources found

Orthologs (12)

1 – 5 of 12

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	collagen type X alpha 1 chain	VGNC:10661	742603
Mouse	collagen, type X, alpha 1	MGI:88445	12813
Rat	collagen type X alpha 1 chain	RGD:2371	25681
Dog	collagen type X alpha 1 chain	VGNC:39455	100856711
Horse	collagen type X alpha 1 chain	VGNC:16720	100066959

Species	Name	OMA	EggNOG	Inparanoid
Chimp	collagen type X alpha 1 chain
Mouse	collagen, type X, alpha 1
Rat	collagen type X alpha 1 chain
Dog	collagen type X alpha 1 chain
Horse	collagen type X alpha 1 chain

Publication Statistics

PubMed Score 182.47

PubMed score by year

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PubTator Score 102.68

PubTator score by year

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Related Publications

Text Mined References (59)

GeneRif Annotations (29)

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10

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PMID	Year	Title