COL20A1
protein-codingcollagen type XX alpha 1 chain, the group of Fibronectin type III domain containing|Collagens
Gene summary
Predicted to be located in endoplasmic reticulum lumen and extracellular matrix. Predicted to be part of collagen type XX trimer. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0019272
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COL20A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020882.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | 4 | |||
| missense | 260 | 26 | 286 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 263 | 28 | 2 | 293 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065933.2 | 34 | MANE Select | |
| Ensembl | ENSP00000351767.6 | 34 | MANE Select | |
| Ensembl | ENSP00000410799.1 | 14 | Standard | |
| Ensembl | ENSP00000414753.1 | 34 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Collagen chain trimerization
- Collagen biosynthesis and modifying enzymes
- Collagen formation
- Extracellular matrix organization
Biological Process
- complement activation, lectin pathway
- growth plate cartilage chondrocyte morphogenesis
Molecular Function
- calcium ion binding
- mannose binding
Cellular Component
- extracellular region
- collagen trimer
- extracellular space
- endoplasmic reticulum lumen
- extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000358894
- Coding exons
- 34
- Length
- 41666
- Individuals with no LoFs
- 124454
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 343
- Defined
- 124798
- p
- 0.00138
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.455 | 778 | 743 | 1.05 | 0.0000471 | 7961 |
| Missense (PolyPhen) | 232 | 235.42 | 0.98545 | 2845 | ||
| Synonymous | -2.49 | 394 | 336 | 1.17 | 0.0000239 | 2787 |
| Loss of Function | 0.189 | 62 | 63.6 | 0.974 | 0.00000349 | 702 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0030 | 0.0029 | notable |
| Latino/Admixed American | 0.0021 | 0.0020 | notable |
| Ashkenazi Jewish | 0.0012 | 0.0012 | notable |
| East Asian | 0.00052 | 0.00050 | rare |
| Finnish | 0.00091 | 0.00088 | rare |
| European (Non-Finnish) | 0.0013 | 0.0013 | notable |
| South Asian | 0.0012 | 0.0011 | notable |
| Other | 0.0021 | 0.0020 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable collagen protein.;
Recessive Scores
- pRec
- 0.0822
Intolerance Scores
- LoFtool
- 0.447
- RVIS EVS
- -0.37
- RVIS percentile EVS
- 28.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.761
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |