COL7A1 collagen type VII alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL7A1provided by HGNC
Official Full Name: collagen type VII alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2214
See related: Ensembl:ENSG00000114270 MIM:120120; AllianceGenome:HGNC:2214
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: EBD1; EBR1; EBDCT; NDNC8
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]
Expression: Biased expression in skin (RPKM 63.4), endometrium (RPKM 13.0) and 5 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 120

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (48564073..48595329, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (48593030..48624289, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (48601506..48632762, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Splice modulation strategy applied to deep intronic variants in COL7A1 causing recessive dystrophic epidermolysis bullosa.
Title: Splice modulation strategy applied to deep intronic variants in COL7A1 causing recessive dystrophic epidermolysis bullosa.
Epidermolysis Bullosa: Two rare case reports of COL7A1 and EBS-GEN SEV KRT14 variants with review of literature.
Title: Epidermolysis Bullosa: Two rare case reports of COL7A1 and EBS-GEN SEV KRT14 variants with review of literature.
Novel variants in LAMA3 and COL7A1 and recurrent variant in KRT5 underlying epidermolysis bullosa in five Chinese families.
Title: Novel variants in LAMA3 and COL7A1 and recurrent variant in KRT5 underlying epidermolysis bullosa in five Chinese families.
COL7A1 G2287R mutation with two clinical phenotypes in the same family: Bullous dermolysis of the newborn and dystrophic epidermolysis bullosa pruriginosa.
Title: COL7A1 G2287R mutation with two clinical phenotypes in the same family: Bullous dermolysis of the newborn and dystrophic epidermolysis bullosa pruriginosa.
Analysis of COL7A1 pathogenic variants in a large cohort of dystrophic epidermolysis bullosa patients from Argentina reveals a new genotype-phenotype correlation.
Title: Analysis of COL7A1 pathogenic variants in a large cohort of dystrophic epidermolysis bullosa patients from Argentina reveals a new genotype-phenotype correlation.
Two cases of the intermediate phenotype of recessive dystrophic epidermolysis bullosa harboring the novel COL7A1 mutation c.3570G>A.
Title: Two cases of the intermediate phenotype of recessive dystrophic epidermolysis bullosa harboring the novel COL7A1 mutation c.3570G>A.
5'RNA Trans-Splicing Repair of COL7A1 Mutant Transcripts in Epidermolysis Bullosa.
Title: 5'RNA Trans-Splicing Repair of COL7A1 Mutant Transcripts in Epidermolysis Bullosa.
Novel and very rare causative variants in the COL7A1 gene of Vietnamese patients with recessive dystrophic epidermolysis bullosa revealed by whole-exome sequencing.
Title: Novel and very rare causative variants in the COL7A1 gene of Vietnamese patients with recessive dystrophic epidermolysis bullosa revealed by whole-exome sequencing.
Ancestral patterns of recessive dystrophic epidermolysis bullosa mutations in Hispanic populations suggest sephardic ancestry.
Title: Ancestral patterns of recessive dystrophic epidermolysis bullosa mutations in Hispanic populations suggest sephardic ancestry.
Prognostic Value of Highly Expressed Type VII Collagen (COL7A1) in Patients With Gastric Cancer.
Title: Prognostic Value of Highly Expressed Type VII Collagen (COL7A1) in Patients With Gastric Cancer.

Submit: New GeneRIF Correction See all GeneRIFs (129)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Dominant dystrophic epidermolysis bullosa with absence of skin MedGen: C0268371 OMIM: 132000 GeneReviews: Dystrophic Epidermolysis Bullosa	Compare labs
Epidermolysis bullosa dystrophica MedGen: C0079294 GeneReviews: Dystrophic Epidermolysis Bullosa	Compare labs
Epidermolysis bullosa pruriginosa MedGen: C1275114 OMIM: 604129 GeneReviews: Dystrophic Epidermolysis Bullosa	Compare labs
Generalized dominant dystrophic epidermolysis bullosa MedGen: C0432322 OMIM: 131750 GeneReviews: Dystrophic Epidermolysis Bullosa	Compare labs
Nonsyndromic congenital nail disorder 8 MedGen: C1843761 OMIM: 607523 GeneReviews: Not available	Compare labs
Pretibial dystrophic epidermolysis bullosa MedGen: C0432321 OMIM: 131850 GeneReviews: Dystrophic Epidermolysis Bullosa	Compare labs
Recessive dystrophic epidermolysis bullosa MedGen: C0079474 OMIM: 226600 GeneReviews: Dystrophic Epidermolysis Bullosa	Compare labs
Transient bullous dermolysis of the newborn MedGen: C1851573 OMIM: 131705 GeneReviews: Dystrophic Epidermolysis Bullosa	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48881 (e-PCR)
- UniSTS:66372

GDB:192955 (e-PCR)
- UniSTS:155734

GDB:192956 (e-PCR)
- UniSTS:155735

GDB:375638 (e-PCR)
- UniSTS:157027

GDB:375655 (e-PCR)
- UniSTS:157028

GDB:375661 (e-PCR)
- UniSTS:157029

GDB:375665 (e-PCR)
- UniSTS:157030

GDB:375668 (e-PCR)
- UniSTS:157031

GDB:375674 (e-PCR)
- UniSTS:157033

RH80100 (e-PCR)
- UniSTS:83603

GDB:371386 (e-PCR)
- UniSTS:156844

GDB:384983 (e-PCR)
- UniSTS:157126

GDB:384984 (e-PCR)
- UniSTS:157127

GDB:384985 (e-PCR)
- UniSTS:157128

GDB:384986 (e-PCR)
- UniSTS:157129

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	ISS Inferred from Sequence or Structural Similarity more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables serine-type endopeptidase inhibitor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in endodermal cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in epidermis development	TAS Traceable Author Statement more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in COPII-coated ER to Golgi transport vesicle	TAS Traceable Author Statement more info
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	IEA Inferred from Electronic Annotation more info
part_of collagen type VII trimer	TAS Traceable Author Statement more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in endoplasmic reticulum-Golgi intermediate compartment membrane	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-1(VII) chain

Names: LC collagen; collagen VII, alpha-1 polypeptide; collagen, type VII, alpha 1; long-chain collagen

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_007065.1 RefSeqGene

Range

5093..36180

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_286

mRNA and Protein(s)

NM_000094.4 → NP_000085.1 collagen alpha-1(VII) chain precursor

See identical proteins and their annotated locations for NP_000085.1

Status: REVIEWED

Source sequence(s)

AC121252

Consensus CDS

CCDS2773.1

UniProtKB/Swiss-Prot

Q02388, Q14054, Q16507

Related

ENSP00000506558.1, ENST00000681320.1

Conserved Domains (6) summary

pfam01391
Location:2108 → 2166

Collagen; Collagen triple helix repeat (20 copies)

cd00063
Location:687 → 771

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd00109
Location:2874 → 2930

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

cd01482
Location:37 → 201

vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...

pfam00041
Location:233 → 317

fn3; Fibronectin type III domain

pfam00092
Location:1054 → 1227

VWA; von Willebrand factor type A domain