Gene Gene information from NCBI Gene database.
Entrez ID 1294
Gene name Collagen type VII alpha 1 chain
Gene symbol COL7A1
Synonyms (NCBI Gene)
EBD1EBDCTEBR1NDNC8
Chromosome 3
Chromosome location 3p21.31
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
SNPs SNP information provided by dbSNP.
163
SNP ID Visualize variation Clinical significance Consequence
rs79378857 G>A Conflicting-interpretations-of-pathogenicity Coding sequence variant, missense variant, non coding transcript variant
rs116005007 C>A Conflicting-interpretations-of-pathogenicity, uncertain-significance Non coding transcript variant, missense variant, coding sequence variant
rs121912828 A>T Pathogenic Non coding transcript variant, missense variant, coding sequence variant, genic downstream transcript variant
rs121912829 C>T Pathogenic Non coding transcript variant, missense variant, coding sequence variant
rs121912830 G>A,T Pathogenic, likely-benign Non coding transcript variant, stop gained, synonymous variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
27
miRTarBase ID miRNA Experiments Reference
MIRT006382 hsa-miR-29c-3p Luciferase reporter assay 21436257
MIRT006382 hsa-miR-29c-3p Luciferase reporter assay 21436257
MIRT006382 hsa-miR-29c-3p Luciferase reporter assay 21436257
MIRT053739 hsa-miR-29b-3p Microarray 22942087
MIRT903179 hsa-miR-1207-5p CLIP-seq
Transcription factors Transcription factors information provided by TRRUST V2 database.
5
Transcription factor Regulation Reference
NFKB1 Unknown 10086338
RELA Unknown 10086338
SMAD3 Unknown 9843964
SMAD4 Unknown 9843964
SP1 Unknown 10980546;9092567
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
25
GO ID Ontology Definition Evidence Reference
GO:0004867 Function Serine-type endopeptidase inhibitor activity IEA
GO:0005515 Function Protein binding IPI 19269366
GO:0005576 Component Extracellular region IEA
GO:0005576 Component Extracellular region TAS
GO:0005581 Component Collagen trimer IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
120120 2214 ENSG00000114270
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q02388
Protein name Collagen alpha-1(VII) chain (Long-chain collagen) (LC collagen)
Protein 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 collage
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00092 VWA 38 209 von Willebrand factor type A domain Domain
PF00041 fn3 233 318 Fibronectin type III domain Domain
PF00041 fn3 331 407 Fibronectin type III domain Domain
PF00041 fn3 419 492 Fibronectin type III domain Domain
PF00041 fn3 509 587 Fibronectin type III domain Domain
PF00041 fn3 599 677 Fibronectin type III domain Domain
PF00041 fn3 687 765 Fibronectin type III domain Domain
PF00041 fn3 777 855 Fibronectin type III domain Domain
PF00041 fn3 868 946 Fibronectin type III domain Domain
PF00092 VWA 1054 1227 von Willebrand factor type A domain Domain
PF01391 Collagen 1251 1310 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 1296 1361 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 1449 1504 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 1489 1548 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2034 2099 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2099 2158 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2257 2321 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2317 2374 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2373 2430 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2407 2465 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2466 2524 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2526 2584 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2563 2639 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2617 2694 Collagen triple helix repeat (20 copies) Repeat
PF01391 Collagen 2722 2787 Collagen triple helix repeat (20 copies) Repeat
PF00014 Kunitz_BPTI 2875 2930 Kunitz/Bovine pancreatic trypsin inhibitor domain Domain
Sequence
MTLRLLVAALCAGILAEAPRVRAQHRERVTCTRLYAADIVFLLDGSSSIGRSNFREVRSF
LEGLVLPFSGAASAQGVRFATVQYSDDPRTEFGLDALGSGGDVIRAIRELSYKGGNTRTG
AAILHVADHVFLPQLARPGVPKVCILITDGKSQDLVDTAAQRLKGQGVKLFAVGIKNADP
EELKRVASQPTSDFFFFVNDFSILRTLLP
LVSRRVCTTAGGVPVTRPPDDSTSAPRDLVL
SEPSSQSLRVQWTAASGPVTGYKVQYTPLTGLGQPLPSERQEVNVPAGETSVRLRGLRPL
TEYQVTVIALYANSIGEA
VSGTARTTALEGPELTIQNTTAHSLLVAWRSVPGATGYRVTW
RVLSGGPTQQQELGPGQGSVLLRDLEPGTDYEVTVSTLFGRSVGPAT
SLMARTDASVEQT
LRPVILGPTSILLSWNLVPEARGYRLEWRRETGLEPPQKVVLPSDVTRYQLDGLQPGTEY
RLTLYTLLEGHE
VATPATVVPTGPELPVSPVTDLQATELPGQRVRVSWSPVPGATQYRII
VRSTQGVERTLVLPGSQTAFDLDDVQAGLSYTVRVSARVGPREGSAS
VLTVRREPETPLA
VPGLRVVVSDATRVRVAWGPVPGASGFRISWSTGSGPESSQTLPPDSTATDITGLQPGTT
YQVAVSVLRGREEGPAA
VIVARTDPLGPVRTVHVTQASSSSVTITWTRVPGATGYRVSWH
SAHGPEKSQLVSGEATVAELDGLEPDTEYTVHVRAHVAGVDGPPA
SVVVRTAPEPVGRVS
RLQILNASSDVLRITWVGVTGATAYRLAWGRSEGGPMRHQILPGNTDSAEIRGLEGGVSY
SVRVTALVGDREGTP
VSIVVTTPPEAPPALGTLHVVQRGEHSLRLRWEPVPRAQGFLLHW
QPEGGQEQSRVLGPELSSYHLDGLEPATQYRVRLSVLGPAGEGPSA
EVTARTESPRVPSI
ELRVVDTSIDSVTLAWTPVSRASSYILSWRPLRGPGQEVPGSPQTLPGISSSQRVTGLEP
GVSYIFSLTPVLDGVRGPEASVTQTPVCPRGLADVVFLPHATQDNAHRAEATRRVLERLV
LALGPLGPQAVQVGLLSYSHRPSPLFPLNGSHDLGIILQRIRDMPYMDPSGNNLGTAVVT
AHRYMLAPDAPGRRQHVPGVMVLLVDEPLRGDIFSPIREAQASGLNVVMLGMAGADPEQL
RRLAPGMDSVQTFFAVDDGPSLDQAVS
GLATALCQASFTTQPRPEPCPVYCPKGQKGEPG
EMGLRGQVGPPGDPGLPGRTGAPGPQGPPGSATAK
GERGFPGADGRPGSPGRAGNPGTPG
APGLKGSPGLPGPRGDPGERGPRGPKGEPGAPGQVIGGEGP
GLPGRKGDPGPSGPPGPRG
PLGDPGPRGPPGLPGTAMKGDKGDRGERGPPGPGEGGIAPGEPGLPGLPGSPGPQGPVGP
PGKKGEKGDSEDGAPGLPGQPGSPGEQGPRGPPGAIGPKGDRGFPGPLGEAGEKGERGPP
GPAG
SRGLPGVAGRPGAKGPEGPPGPTGRQGEKGEPGRPGDPAVVGPA
VAGPKGEKGDVG
PAGPRGATGVQGERGPPGLVLPGDPGPKGDPGDRGPIGLTGRAGPPGDSGPPGEKGDPGR
PGPPGPVGPRGRDGEVGEKGDEGPPGDPGLPGKAGERGLRGAPGVRGPVGEKGDQGDPGE
DGRNGSPGSSGPKGDRGEPGPPGPPGRLVDTGPGAREKGEPGDRGQEGPRGPKGDPGLPG
APGERGIEGFRGPPGPQGDPGVRGPAGEKGDRGPPGLDGRSGLDGKPGAAGPSGPNGAAG
KAGDPGRDGLPGLRGEQGLPGPSGPPGLPGKPGEDGKPGLNGKNGEPGDPGEDGRKGEKG
DSGASGREGRDGPKGERGAPGILGPQGPPGLPGPVGPPGQGFPGVPGGTGPKGDRGETGS
KGEQGLPGERGLRGEPGSVPNVDRLLETAGIKASALREIVETWDESSGSFLPVPERRRGP
KGDSGEQGPPGKEGPIGFPGERGLKGDRGDPGPQGPPGLALGERGPPGPSGLAGEPGKPG
IPGLPGRAGGVGEAGRPGERGERGEKGERGEQGRDGPPGLPGTPGPPGPPGPKVSVDE
PG
PGLSGEQGPPGLKGAKGEPGSNGDQGPKGDRGVPGIKGDRGEPGPRGQDGNPGLPGER
GM
AGPEGKPGLQGPRGPPGPVGGHGDPGPPGAPGLAGPAGPQGPSGLKGEPGETGPPGRGLT
GPTGAVGLPGPPGPSGLVGPQGSPGLPGQVGETGKPGAPGRDGASGKDGDRGSPGVPGSP
GLPGPVGPKGEPGPTGAPGQAVVGLPGAKGEKGAPG
GLAGDLVGEPGAKGDRGLPGPRGE
KGEAGRAGEPGDPGEDGQKGAPGPKGFKGDPGVGVPGSPGPPGPPGVKGDLGLPGLPGAP
GVVGFPGQTGPRGEMGQPGPSGERGLAGPPGREGIPGPLGPPGPPGSVGPPGASGLKGDK
GDPGV
GLPGPRGERGEPGIRGEDGRPGQEGPRGLTGPPGSRGERGEKGDVGSAGLKGDKG
DSAV
ILGPPGPRGAKGDMGERGPRGLDGDKGPRGDNGDPGDKGSKGEPGDKGSAGLPGLR
GLLG
PQGQPGAAGIPGDPGSPGKDGVPGIRGEKGDVGFMGPRGLKGERGVKGACGLDGEK
GDKGEAGPPGRPGLAGHKGEMGEPGVPGQSGAPGKEGLIGPKGDRGFDGQPGPK
GDQGEK
GERGTPGIGGFPGPSGNDGSAGPPGPPGSVGPRGPEGLQGQKGERGPPGERVVGAPGVPG
APGERGEQGRPGPAGPRGEKGEAALTE
DDIRGFVRQEMSQHCACQGQFIASGSRPLPSYA
ADTAGSQLHAVPVLRVSHAEEEERVPPEDDEYSEYSEYSVEEYQDPEAPWDSDDPCSLPL
DEGSCTAYTLRWYHRAVTGSTEACHPFVYGGCGGNANRFGTREACERRCP
PRVVQSQGTG
TAQD
Sequence length 2944
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Protein digestion and absorption   Collagen degradation
Extracellular matrix organization
Collagen biosynthesis and modifying enzymes
Assembly of collagen fibrils and other multimeric structures
COPII-mediated vesicle transport
Integrin cell surface interactions
Anchoring fibril formation
Laminin interactions
Cargo concentration in the ER
Collagen chain trimerization
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
88
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormal blistering of the skin Likely pathogenic; Pathogenic rs121912855, rs780261665 RCV000626608
RCV000626602
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Abnormality of the skin Likely pathogenic; Pathogenic rs2107667545, rs2044195570, rs2107755031, rs780261665, rs121912856, rs767539005 RCV001814535
RCV001814492
RCV001814565
RCV000626601
RCV000626605
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
COL7A1-related disorder Pathogenic; Likely pathogenic rs759949767, rs765529435, rs1560232515, rs2107718927, rs759634066, rs748940147, rs2107671960, rs2107660525, rs2107633400, rs2107631988, rs2107641787, rs753368984, rs1261268687, rs757715378, rs2107661505
View all (44 more)
RCV003405591
RCV004528479
RCV004545222
RCV004531193
RCV003898367
View all (56 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Dominant dystrophic epidermolysis bullosa with absence of skin Pathogenic rs121912841, rs121912832, rs762162799 RCV000144373
RCV000018976
RCV004786689
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Abnormality of the thyroid gland Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ACRAL DYSTROPHIC EPIDERMOLYSIS BULLOSA GenCC
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AMELOGENESIS IMPERFECTA LOCAL HYPOPLASTIC FORM Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Amelogenesis imperfecta type 1 Conflicting classifications of pathogenicity; Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acral dystrophic epidermolysis bullosa Acral Dystrophic Epidermolysis Bullosa ORPHANET_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Alopecia Alopecia HPO_DG
★☆☆☆☆
Found in Text Mining only
Amyloidosis Amyloidosis Pubtator 25566895 Associate
★☆☆☆☆
Found in Text Mining only
amyloidosis IX Amyloidosis Pubtator 25566895 Associate
★☆☆☆☆
Found in Text Mining only
Anemia Anemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Anemia Aplastic Aplastic anemia Pubtator 9284109 Associate
★☆☆☆☆
Found in Text Mining only
Ankyloglossia Ankyloglossia HPO_DG
★☆☆☆☆
Found in Text Mining only
Aortic Valve Insufficiency Aortic Valve Insufficiency BEFREE 12558638
★☆☆☆☆
Found in Text Mining only
Aortic Valve Insufficiency Aortic valve disease Pubtator 12558638 Associate
★☆☆☆☆
Found in Text Mining only
Aplasia Cutis Congenita Aplasia Cutis Congenita BEFREE 24252097
★☆☆☆☆
Found in Text Mining only