COL7A1
protein-codingcollagen type VII alpha 1 chain, the group of Fibronectin type III domain containing|Collagens|MicroRNA protein coding host genes
Gene summary
This gene encodes the alpha chain of type VII collagen. The type VII collagen fibril, composed of three identical alpha collagen chains, is restricted to the basement zone beneath stratified squamous epithelia. It functions as an anchoring fibril between the external epithelia and the underlying stroma. Mutations in this gene are associated with all forms of dystrophic epidermolysis bullosa. In the absence of mutations, however, an acquired form of this disease can result from an autoimmune response made to type VII collagen. [provided by RefSeq, Jul 2008]
- EBDCT
- EBD1
- EBR1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007549
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0007557
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007552
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0011398
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0009179
Submitter: ClinGen
The dystrophic epidermolysis bullosa (DEB) disorders can be divided into recessive (RDEB, MONDO:0009179) and dominant (DDEB, MONDO:0002529). The RDEB is the most severe form of epidermolysis bullosa (EB). It is caused by biallelic pathogenic variants in the collage VII gene COL7A1. Patients with RDEB have up to 50 fold increased incidence of cutaneous squamous cell carcinoma (SCC) (PMID: 26083672). Clinically, the risk of developing SCC appears to parallel the severity, extent of ulceration and scarring of the skin, which in turn correlates with loss of collagen VII expression and decreased or absent anchoring fibrils. Loss-of-function mutations in COL7A1 in RDEB patients lead to dermal-epidermal tissue separation as a consequence of impaired interactions with major dermal epidermal junction (DEJ) components. More than 700 COL7A1 recessive DEB-causing variants spanning the entire gene have been described for all forms of DEB. Homozygous loss of function variants from a large study on 152 Iranian families with 238 patients of DEB (PMID: 27899325) and a small study (PMID: 26864810) are recorded in this curation for genetic evidence (12 points). This gene-disease association is also supported by experimental evidence (6 points). A knockdown shCOL7 SCC-IC1 cell line demonstrated loss of COL7 reduced differentiation, increased VEGF expression, angiogenesis and invasion in shCOL7 xenografts similar to that seen in RDEB patients (PMID: 26476432). COL7A1-null mice die too early to initiate cancer studies (PMID: 10523500). A collagen VII hypomorphic mouse, homozygous Col7a1flNeo/flNeo mice, as an immunocompetent animal model for DEB showed expression of collagen VII at about 10% of normal levels, and their phenotype closely resembled characteristics of severe human DEB, including mucocutaneous blistering, nail dystrophy, and mitten deformities of the extremities. Wildtype fibroblast injection restored Collagen VII deposition and function at the DEJZ (PubMed: 18382769). In addition, an ABEmax (adenine base editor) corrected endogenous COL7A1 in autologous cells [patient derived fibroblasts and induced pluripotent stem cells (iPSCs)] can restore normalized epithelial architecture via increased COL7 expression (PMID: 31437443). In summary, both genetic and extensive experimental evidence demonstrate that COL7A1 is definitely associated with autosomal recessively inherited Dystrophic Epidermolysis Bullosa (DEB), which is associated with increased risk of developing squamous cell carcinoma (SCC). This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time.
Inheritance Pattern: AD
Disease ID:MONDO:0007549
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0009179
Submitter: Natera
Inheritance Pattern: AD
Disease ID:MONDO:0007549
Submitter: Natera
Inheritance Pattern: AD
Disease ID:MONDO:0007557
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0015552
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011398
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0009179
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009179
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007552
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0015553
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007549
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0007552
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0007548
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0019522
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007548
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0019310
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009179
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009179
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0011398
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0009179
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011398
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007557
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0007548
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
Manifestation: Dermatologic
Intervention: Dermatologic
Rationale: A topical gene therapy has been approved for treatment of forms of dystrophic epidermolysis bullosa
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COL7A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000094.4. 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 | 5 | 12 | 72 | 1405 | 1 | 1495 |
| missense | 135 | 246 | 1390 | 402 | 19 | 2192 |
| nonsense | 145 | 39 | 1 | 185 | ||
| start loss | 3 | 3 | ||||
| frameshift | 301 | 92 | 1 | 394 | ||
| splice donor/acceptor (+/-2bp) | 69 | 216 | 27 | 1 | 313 | |
| Total | 658 | 605 | 1491 | 1808 | 20 | 4582 |
Highest pathogenic variant AF is 0.00023722817
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000085.1 | 118 | MANE Select | |
| Ensembl | ENSP00000506558.1 | 118 | MANE Select | |
| Ensembl | ENSP00000332371.8 | 118 | Standard | |
| Ensembl | ENSP00000332371.8 | 118 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein digestion and absorption - Homo sapiens (human)
- Assembly of collagen fibrils and other multimeric structures
- Vesicle-mediated transport
- Membrane Trafficking
- Collagen chain trimerization
Biological Process
- growth plate cartilage chondrocyte morphogenesis
- endoplasmic reticulum to Golgi vesicle-mediated transport
- cell adhesion
- epidermis development
- negative regulation of endopeptidase activity
Molecular Function
- serine-type endopeptidase inhibitor activity
- protein binding
- extracellular matrix structural constituent conferring tensile strength
Cellular Component
- Golgi membrane
- extracellular region
- collagen type VII trimer
- basement membrane
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000328333
- Coding exons
- 118
- Length
- 31195
- Individuals with no LoFs
- 124974
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 772
- Defined
- 125748
- p
- 0.00308
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 1594 | 1.78e+3 | 0.894 | 0.000123 | 18151 |
| Missense (PolyPhen) | 195 | 260.01 | 0.74996 | 2620 | ||
| Synonymous | 0.407 | 658 | 671 | 0.980 | 0.0000440 | 6645 |
| Loss of Function | 6.48 | 100 | 199 | 0.504 | 0.0000119 | 2205 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00057 | 0.00055 | rare |
| Latino/Admixed American | 0.0016 | 0.0016 | notable |
| Ashkenazi Jewish | 0.0018 | 0.0018 | notable |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.014 | 0.012 | notable |
| European (Non-Finnish) | 0.0023 | 0.0022 | notable |
| South Asian | 0.0045 | 0.0046 | notable |
| Other | 0.0034 | 0.0033 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Stratified squamous epithelial basement membrane protein that forms anchoring fibrils which may contribute to epithelial basement membrane organization and adherence by interacting with extracellular matrix (ECM) proteins such as type IV collagen.;
- Disease
- DISEASE: Note=Epidermolysis bullosa acquisita (EBA) is an autoimmune acquired blistering skin disease resulting from autoantibodies to type VII collagen.; DISEASE: Epidermolysis bullosa dystrophica, autosomal dominant (DDEB) [MIM:131750]: A group of autosomal dominant blistering skin diseases characterized by tissue separation which occurs below the dermal-epidermal basement membrane at the level of the anchoring fibrils. Various clinical types with different severity are recognized, ranging from severe mutilating forms to mild forms with limited and localized scarring, and less frequent extracutaneous manifestations. {ECO:0000269|PubMed:10084325, ECO:0000269|PubMed:10232406, ECO:0000269|PubMed:10232407, ECO:0000269|PubMed:10232408, ECO:0000269|PubMed:10233777, ECO:0000269|PubMed:10836608, ECO:0000269|PubMed:11142768, ECO:0000269|PubMed:20598510, ECO:0000269|PubMed:7861014, ECO:0000269|PubMed:8170945, ECO:0000269|PubMed:9215684, ECO:0000269|PubMed:9668111, ECO:0000269|PubMed:9740253, ECO:0000269|PubMed:9856843}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa dystrophica, autosomal recessive (RDEB) [MIM:226600]: A group of autosomal recessive blistering skin diseases characterized by tissue separation which occurs below the dermal-epidermal basement membrane at the level of the anchoring fibrils. Various clinical types with different severity are recognized, ranging from severe mutilating forms, such as epidermolysis bullosa dystrophica Hallopeau-Siemens type, to mild forms with limited localized scarring and less frequent extracutaneous manifestations. Mild forms include epidermolysis bullosa mitis and epidermolysis bullosa localisata. {ECO:0000269|PubMed:10084325, ECO:0000269|PubMed:10620140, ECO:0000269|PubMed:11167698, ECO:0000269|PubMed:12787275, ECO:0000269|PubMed:20598510, ECO:0000269|PubMed:8513326, ECO:0000269|PubMed:8592061, ECO:0000269|PubMed:8618018, ECO:0000269|PubMed:8757758, ECO:0000269|PubMed:9215684, ECO:0000269|PubMed:9326325, ECO:0000269|PubMed:9444387, ECO:0000269|PubMed:9740253, ECO:0000269|PubMed:9804332}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Transient bullous dermolysis of the newborn (TBDN) [MIM:131705]: TBDN is a neonatal form of dystrophic epidermolysis bullosa characterized by sub-epidermal blisters, reduced or abnormal anchoring fibrils at the dermo-epidermal junction, and electron-dense inclusions in keratinocytes. TBDN heals spontaneously or strongly improves within the first months and years of life. {ECO:0000269|PubMed:9856844}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa dystrophica, pretibial type (PR- DEB) [MIM:131850]: A form of dystrophic epidermolysis bullosa characterized by pretibial blisters that develop into prurigo-like hyperkeratotic lesions. It predominantly affects the pretibial areas, sparing the knees and other parts of the skin. Other clinical features include nail dystrophy, albopapuloid skin lesions, and hypertrophic scars without pretibial predominance. The phenotype shows considerable interindividual variability. Inheritance is autosomal dominant. {ECO:0000269|PubMed:8541842}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa dystrophica, Bart type (B-DEB) [MIM:132000]: An autosomal dominant form of dystrophic epidermolysis bullosa characterized by congenital localized absence of skin, skin fragility and deformity of nails. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa pruriginosa (EBP) [MIM:604129]: A distinct clinical subtype of epidermolysis bullosa dystrophica. It is characterized by skin fragility, blistering, scar formation, intense pruritus and excoriated prurigo nodules. Onset is in early childhood, but in some cases is delayed until the second or third decade of life. Inheritance can be autosomal dominant or recessive. {ECO:0000269|PubMed:10383749, ECO:0000269|PubMed:11142768}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Nail disorder, non-syndromic congenital, 8 (NDNC8) [MIM:607523]: A nail disorder characterized by isolated toenail dystrophy. The nail changes are most severe in the great toes and consist of the nail plate being buried in the nail bed with a deformed and narrow free edge. {ECO:0000269|PubMed:11843659}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa dystrophica, with subcorneal cleavage (EBDSC) [MIM:131750]: A bullous skin disorder with variable sized clefts just beneath the level of the stratum corneum. Clinical features include blisters, milia, atrophic scarring, nail dystrophy, and oral and conjunctival involvement, as seen in dystrophic epidermolysis bullosa. {ECO:0000269|PubMed:11874498, ECO:0000269|PubMed:2653224}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.253
Intolerance Scores
- LoFtool
- 0.0371
- RVIS EVS
- -4.24
- RVIS percentile EVS
- 0.13
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.790
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |