COL7A1

protein-coding

collagen 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]

Previous symbols:
  • EBDCT
  • EBD1
  • EBR1

MANE transcript

NM_000094.4

Inheritance

AD, AR

ClinVar variants

P:1263U:1491B:1828

Top phenotype

Epidermolysis bullosa dystrophica, autosomal dominant; Epidermolysis bullosa dystrophica, autosomal recessive; Epidermolysis bullosa dystrophica inversia; Epidermolysis bullosa pruriginosa; Nail disorder, nonsyndromic congenital, 8; Epidermolysis bullosa dystrophica, with congenital localized absence of skin and deformity of nails; Epidermolysis bullosa, pretibial; Transient bullous dermolysis of the newborn

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr3:48,564,073-48,595,329

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~31.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

generalized dominant dystrophic epidermolysis bullosaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007549

Submitter: Labcorp Genetics (formerly Invitae)

epidermolysis bullosa with congenital localized absence of skin and deformity of nailsSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0007557

Submitter: Labcorp Genetics (formerly Invitae)

pretibial dystrophic epidermolysis bullosaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007552

Submitter: Genomics England PanelApp

dystrophic epidermolysis bullosa pruriginosaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011398

Submitter: Genomics England PanelApp

recessive dystrophic epidermolysis bullosaDEFINITIVE

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.

generalized dominant dystrophic epidermolysis bullosaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007549

Submitter: Genomics England PanelApp

recessive dystrophic epidermolysis bullosaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009179

Submitter: Natera

generalized dominant dystrophic epidermolysis bullosaDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007549

Submitter: Natera

epidermolysis bullosa with congenital localized absence of skin and deformity of nailsDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007557

Submitter: G2P

acral dystrophic epidermolysis bullosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015552

Submitter: Orphanet

dystrophic epidermolysis bullosa pruriginosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011398

Submitter: Orphanet

recessive dystrophic epidermolysis bullosaDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009179

Submitter: G2P

recessive dystrophic epidermolysis bullosaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009179

Submitter: Orphanet

pretibial dystrophic epidermolysis bullosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007552

Submitter: Orphanet

dystrophic epidermolysis bullosa, nails onlySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015553

Submitter: Orphanet

generalized dominant dystrophic epidermolysis bullosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007549

Submitter: Orphanet

pretibial dystrophic epidermolysis bullosaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0007552

Submitter: Genomics England PanelApp

transient bullous dermolysis of the newbornSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0007548

Submitter: Genomics England PanelApp

recessive dystrophic epidermolysis bullosa-generalized otherSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019522

Submitter: Orphanet

transient bullous dermolysis of the newbornSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007548

Submitter: Orphanet

recessive dystrophic epidermolysis bullosa inversaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019310

Submitter: Orphanet

recessive dystrophic epidermolysis bullosaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009179

Submitter: G2P

recessive dystrophic epidermolysis bullosaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009179

Submitter: Genomics England PanelApp

dystrophic epidermolysis bullosa pruriginosaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011398

Submitter: Genomics England PanelApp

recessive dystrophic epidermolysis bullosaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009179

Submitter: Ambry Genetics

dystrophic epidermolysis bullosa pruriginosaDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011398

Submitter: G2P

epidermolysis bullosa with congenital localized absence of skin and deformity of nailsSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007557

Submitter: Genomics England PanelApp

transient bullous dermolysis of the newbornSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007548

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Epidermolysis bullosa dystrophica, autosomal dominant; Epidermolysis bullosa dystrophica, autosomal recessive; Epidermolysis bullosa dystrophica inversia; Epidermolysis bullosa pruriginosa; Nail disorder, nonsyndromic congenital, 8; Epidermolysis bullosa dystrophica, with congenital localized absence of skin and deformity of nails; Epidermolysis bullosa, pretibial; Transient bullous dermolysis of the newbornAD/AR

Manifestation: Dermatologic

Intervention: Dermatologic

Rationale: A topical gene therapy has been approved for treatment of forms of dystrophic epidermolysis bullosa

Refs: 1347297; 1680286; 8513326; 8345225; 8245264; 8170945; 8037207; 8541842; 7577595; 8644729; 9406826; 9347800; 9182828; 9856844; 9892921; 10583163; 10383749; 10469344; 12485454; 11874498; 11843659; 12787275; 16225626; 16965329; 17434045; 16971478; 20574443; 20920254; 21113014; 21182502; 21196708; 21352278; 21382783; 21574979; 21629976; 21849769; 21967228; 22058051; 22266148; 22515571; 22854212; 22909362; 22974128; 23013315; 35347281; 36516090Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COL7A1 variants in ClinVar

49 Conditions Cataloged
not providedTotal: 5406
Epidermolysis bullosa dystrophicaTotal: 872
Recessive dystrophic epidermolysis bullosaTotal: 735
not specifiedTotal: 497
Inborn genetic diseasesTotal: 466
COL7A1-related disorderTotal: 318
Generalized dominant dystrophic epidermolysis bullosaTotal: 307
Transient bullous dermolysis of the newbornTotal: 267

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
12
clinvar
72
clinvar
1405
clinvar
1
clinvar
1495
missense
135
clinvar
246
clinvar
1390
clinvar
402
clinvar
19
clinvar
2192
nonsense
145
clinvar
39
clinvar
1
clinvar
185
start loss
3
clinvar
3
frameshift
301
clinvar
92
clinvar
1
clinvar
394
splice donor/acceptor (+/-2bp)
69
clinvar
216
clinvar
27
clinvar
1
clinvar
313
Total65860514911808204582

Highest pathogenic variant AF is 0.00023722817

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000094.4RefSeqNP_000085.1118MANE Select
ENST00000681320.1EnsemblENSP00000506558.1118MANE Select
ENST00000328333.12EnsemblENSP00000332371.8118Standard
ENST00000328333.13EnsemblENSP00000332371.8118Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.5915941.78e+30.8940.00012318151
Missense (PolyPhen)195260.010.749962620
Synonymous0.4076586710.9800.00004406645
Loss of Function6.481001990.5040.00001192205

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000570.00055rare
Latino/Admixed American0.00160.0016notable
Ashkenazi Jewish0.00180.0018notable
East Asian0.00130.0013notable
Finnish0.0140.012notable
European (Non-Finnish)0.00230.0022notable
South Asian0.00450.0046notable
Other0.00340.0033notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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