COL5A2
protein-codingcollagen type V alpha 2 chain, the group of Collagens|MicroRNA protein coding host genes
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 associated with Ehlers-Danlos syndrome, types I and II. [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 ~193.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0019568
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0019568
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0020066
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007522
Submitter: ClinGen
COL5A2 was first reported in relation to autosomal dominant Ehlers-Danlos syndrome (EDS), classic type, in 1998 (Michalickova et al, PMID: 9425231; Richards et al, PMID: 9783710). First described by Beighton in 1968, classic EDS (formerly known as EDS type I or “gravis” and type II or “mitis”) is a connective tissue disorder characterized by joint hypermobility, skin hyperextensibilty, and skin fragility leading to atrophic scarring (reviewed in Bowen et al, 2017, PMID: 28192633; Malfait et al, 2018, PMID 20301422). This curation includes nineteen unique variants (splicing variants causing in frame deletions, missense variants, one in frame deletion/insertion, and a 3’ terminal frameshift not expected to undergo nonsense-mediated decay) that have been reported in nineteen probands meeting clinical criteria for classic EDS in six publications (Michalickova et al, 1998, PMID: 9425231; Richards et al, 1998, PMID: 9783710; Malfait et al, 2005, PMID: 15580559; Symoens et al, 2012, PMID: 22696272; Ritelli et al, 2013, PMID: 23587214, Watanabe et al, 2016, PMID: 27656288). Of note, none of these variants is predicted to result in lack of protein. Like the other fibrillar collagens, alpha2(V) has a long uninterrupted triple helix of Gly-X-Y repeats. The glycine residues have been shown to be important to the triple helix structure (Long et al, 1993, PMID 8218237; Bella et al, 1994, PMID 7695699; Shoulders and Raines, 2009, PMID 19344236). Ten of the variants curated here cause in frame deletion of 18-36 amino acids in the helical domain, and one is an in frame insertion/deletion. With the exception of one frameshift in the 3’ end of the gene, all of the other variants curated involved missense substitutions of a glycine residue in the helical domain. Alteration or loss of the Gly-X-Y repeats in the helical region is expected to result in a dominant-negative mechanism of disease, with up to 50% of Collagen V chains incorporating an altered alpha2(V) chain. The relationship between COL5A2 and classic EDS is also supported by experimental evidence. This includes the biochemical function of COL5A2 in regulating collagen fiber size in the extra-cellular matrix, which is consistent with the clinical features of the condition (Andrikopoulos et al., 1995, PMID: 7704020; Fichard et al, 1995, PMID: 8535602; the interaction of the gene product of COL5A2 (alpha2(V)) in a triple helical structure with the gene product of COL5A1 (alpha1(V), another gene with a definitive relationship with classic EDS (Bentz H, et al., 1978, PMID: 738278); functional alteration evidence in which fibroblasts and dermis samples from a patient with classic EDS and a COL5A2 variant show abnormalities in collagen solubility and collagen fibril size (Michalickova et al, 1998, PMID: 9425231); the clinical features of animal models including a cow model with skin abnormalities and a COL5A2 variant (Jacinto et al, 2020, PMID: 33143196), a conditional mouse knockout with fragile skin and poor wound-healing (Park et al, 2017, PMID: 28734943), and mouse model with an in frame deletion of the N-telopeptide domain in which homozygotes have fragile, hyperextensible skin (Andrikopoulos et al, 1995, PMID: 7704020). In summary, COL5A2 is definitively associated with autosomal dominant classic EDS. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This gene-disease classification was approved by the General Gene Curation Expert panel on March 24th, 2021.
Inheritance Pattern: AD
Disease ID:MONDO:0007522
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Dermatologic; Musculoskeletal; Obstetric; Ophthalmologic
Intervention: Cardiovascular; Obstetric
Rationale: Individuals may have aortic root dilatation, but the natural history is unclear, and may not typically progress, though yearly surveillance with echocardiogram when aortic dilatation or mitral valve prolapse is peresent has been recommended; Precautions in pregnancy may be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COL5A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000393.5. 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 | 1 | 2 | 19 | 445 | 9 | 476 |
| missense | 3 | 29 | 819 | 219 | 10 | 1080 |
| nonsense | 3 | 6 | 9 | |||
| start loss | 1 | 1 | ||||
| frameshift | 5 | 4 | 6 | 15 | ||
| splice donor/acceptor (+/-2bp) | 7 | 16 | 23 | 46 | ||
| Total | 19 | 51 | 874 | 664 | 19 | 1627 |
Highest pathogenic variant AF is 0.000047903446
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000384.2 | 54 | MANE Select | |
| Ensembl | ENSP00000364000.3 | 54 | MANE Select | |
| Ensembl | ENSP00000482184.1 | 40 | Standard | |
| Ensembl | ENSP00000482184.1 | 40 | 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
- skeletal system development
- ossification
- extracellular matrix organization
- collagen fibril organization
- notochord development
Molecular Function
- extracellular matrix structural constituent
- extracellular matrix structural constituent conferring tensile strength
- SMAD binding
- metal ion binding
Cellular Component
- extracellular region
- collagen trimer
- collagen type V trimer
- extracellular space
- endoplasmic reticulum lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000374866
- Coding exons
- 54
- Length
- 147984
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 21
- Defined
- 125746
- p
- 0.0000835
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.44 | 679 | 883 | 0.769 | 0.0000484 | 9373 |
| Missense (PolyPhen) | 165 | 259.94 | 0.63475 | 2644 | ||
| Synonymous | 0.160 | 273 | 276 | 0.988 | 0.0000151 | 3279 |
| Loss of Function | 8.63 | 4 | 94.5 | 0.0423 | 0.00000513 | 1113 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
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. Type V collagen is a key determinant in the assembly of tissue- specific matrices (By similarity). {ECO:0000250}.;
- Disease
- DISEASE: Ehlers-Danlos syndrome, classic type, 2 (EDSCL2) [MIM:130010]: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. The main features of classic Ehlers-Danlos syndrome are joint hypermobility and dislocation, and fragile, bruisable skin. EDSCL2 inheritance is autosomal dominant. {ECO:0000269|PubMed:27656288, ECO:0000269|PubMed:9425231, ECO:0000269|PubMed:9783710}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.391
Intolerance Scores
- LoFtool
- 0.00489
- RVIS EVS
- -0.87
- RVIS percentile EVS
- 10.59
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.331
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |