COL5A3
protein-codingcollagen type V alpha 3 chain, the group of Collagens
Gene summary
This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are thought to be responsible for the symptoms of a subset of patients with Ehlers-Danlos syndrome type III. Messages of several sizes can be detected in northern blots but sequence information cannot confirm the identity of the shorter messages. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COL5A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015719.4. 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 | 8 | 6 | 2 | 16 | ||
| missense | 281 | 18 | 2 | 301 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 10 | 10 | ||||
| Total | 0 | 0 | 300 | 24 | 4 | 328 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056534.2 | 67 | MANE Select | |
| Ensembl | ENSP00000264828.3 | 67 | MANE Select | |
| Ensembl | ENSP00000803661.1 | 67 | Standard | |
| RefSeq | XP_011526344.1 | 67 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein digestion and absorption - Homo sapiens (human)
- miRNA targets in ECM and membrane receptors
- Focal Adhesion
- Focal Adhesion-PI3K-Akt-mTOR-signaling pathway
- Collagen chain trimerization
Biological Process
- cell adhesion
- cell-matrix adhesion
- extracellular matrix organization
- collagen fibril organization
- skin development
Molecular Function
- extracellular matrix structural constituent
- collagen binding
- heparin binding
- extracellular matrix structural constituent conferring tensile strength
- proteoglycan binding
Cellular Component
- extracellular region
- collagen type V trimer
- extracellular space
- endoplasmic reticulum lumen
- extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264828
- Coding exons
- 67
- Length
- 50911
- Individuals with no LoFs
- 125585
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 163
- Defined
- 125748
- p
- 0.000648
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.492 | 946 | 990 | 0.956 | 0.0000583 | 10773 |
| Missense (PolyPhen) | 63 | 81.671 | 0.77138 | 799 | ||
| Synonymous | 0.317 | 386 | 394 | 0.980 | 0.0000240 | 3841 |
| Loss of Function | 4.99 | 51 | 107 | 0.479 | 0.00000533 | 1258 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00057 | 0.00052 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00074 | 0.00071 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00066 | 0.00063 | rare |
| South Asian | 0.0017 | 0.0015 | notable |
| Other | 0.0010 | 0.00098 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin.;
Intolerance Scores
- LoFtool
- 0.0606
- RVIS EVS
- 0.14
- RVIS percentile EVS
- 63.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |