COL5A1 collagen type V alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL5A1provided by HGNC
Official Full Name: collagen type V alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2209
See related: Ensembl:ENSG00000130635 MIM:120215; AllianceGenome:HGNC:2209
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: EDSC; FMDMF; EDSCL1
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. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
Expression: Broad expression in placenta (RPKM 45.0), endometrium (RPKM 38.1) and 16 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 9q34.3

Exon count:: 68

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (134641803..134844843)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (146859174..147065950)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (137533649..137736689)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

COL5A1 overexpression correlates with poor prognosis in human cervical cancer.
Title: COL5A1 overexpression correlates with poor prognosis in human cervical cancer.
CircCOL5A1 is involved in proliferation, invasion, and inhibition of ferroptosis of colorectal cancer cells via miR-1287-5p/SLC7A11.
Title: CircCOL5A1 is involved in proliferation, invasion, and inhibition of ferroptosis of colorectal cancer cells via miR-1287-5p/SLC7A11.
The Association of a Single Nucleotide Variant in COL5A1 to Early Onset Keratoconus and Pectus Excavatum-Convergence of Extracellular Matrix Pathologies.
Title: The Association of a Single Nucleotide Variant in COL5A1 to Early Onset Keratoconus and Pectus Excavatum-Convergence of Extracellular Matrix Pathologies.
COL5A1 promotes triple-negative breast cancer progression by activating tumor cell-macrophage crosstalk.
Title: COL5A1 promotes triple-negative breast cancer progression by activating tumor cell-macrophage crosstalk.
Clinical significance of polymorphisms of genes encoding collagen (COL1A1, COL5A1) and their correlation with joint laxity and recurrent patellar dislocation in adolescents.
Title: Clinical significance of polymorphisms of genes encoding collagen (COL1A1, COL5A1) and their correlation with joint laxity and recurrent patellar dislocation in adolescents.
Association Between COL5a1, COL11a1, and COL11a2 Gene Variations and Rotator Cuff Tendinopathy in Young Athletes.
Title: Association Between COL5a1, COL11a1, and COL11a2 Gene Variations and Rotator Cuff Tendinopathy in Young Athletes.
LncRNA BBOX1-AS1 Contributes to the Progression of Esophageal Carcinoma by Targeting the miR-361-3p/COL5A1 Axis.
Title: LncRNA BBOX1-AS1 Contributes to the Progression of Esophageal Carcinoma by Targeting the miR-361-3p/COL5A1 Axis.
LINC00173 blocks GATA6-mediated transcription of COL5A1 to affect malignant development of oral squamous cell carcinoma.
Title: LINC00173 blocks GATA6-mediated transcription of COL5A1 to affect malignant development of oral squamous cell carcinoma.
Genetic variants within the COL5A1 gene are associated with ligament injuries in physically active populations from Australia, South Africa, and Japan.
Title: Genetic variants within the COL5A1 gene are associated with ligament injuries in physically active populations from Australia, South Africa, and Japan.
Sex Differences in the Association between Risk of Anterior Cruciate Ligament Rupture and COL5A1 Polymorphisms in Elite Footballers.
Title: Sex Differences in the Association between Risk of Anterior Cruciate Ligament Rupture and COL5A1 Polymorphisms in Elite Footballers.

Submit: New GeneRIF Correction See all GeneRIFs (104)

Phenotypes

Go to the top of the page Help

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
Ehlers-Danlos syndrome, classic type, 1 MedGen: C0268335 OMIM: 130000 GeneReviews: Classic Ehlers-Danlos Syndrome	not available
Fibromuscular dysplasia, multifocal MedGen: C5543412 OMIM: 619329 GeneReviews: Not available	not available

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2017-12-14) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2017-12-14) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study of central corneal thickness in Latinos. EBI GWAS Catalog EBI GWAS CatalogPubMed
Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. EBI GWAS Catalog EBI GWAS CatalogPubMed
Joint influence of small-effect genetic variants on human longevity. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multidimensional prognostic risk assessment identifies association between IL12B variation and surgery in Crohn's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
New loci associated with central cornea thickness include COL5A1, AKAP13 and AVGR8. EBI GWAS Catalog EBI GWAS CatalogPubMed
Population-based meta-analysis in Caucasians confirms association with COL5A1 and ZNF469 but not COL8A2 with central corneal thickness. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Replication interactions

Interaction	Pubs
Knockdown of collagen, type V, alpha 1 (COL5A1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH45344 (e-PCR)
- UniSTS:82444

G54670 (e-PCR)
- UniSTS:117775

SHGC-143900 (e-PCR)
- UniSTS:174103

D8S2279 (e-PCR)
- UniSTS:473907

RH101994 (e-PCR)
- UniSTS:96328

RH93484 (e-PCR)
- UniSTS:90709

SHGC-147947 (e-PCR)
- UniSTS:172903

RH76754 (e-PCR)
- UniSTS:85105

D13S1553 (e-PCR)
- UniSTS:473482

RH70027 (e-PCR)
- UniSTS:20889

RH75751 (e-PCR)
- UniSTS:92062

RH70759 (e-PCR)
- UniSTS:8111

COL5A1_2419 (e-PCR)
- UniSTS:463574

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	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	IDA Inferred from Direct Assay more info	PubMed
enables integrin binding	NAS Non-traceable Author Statement more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables proteoglycan binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in blood vessel development	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen fibril organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen fibril organization	NAS Non-traceable Author Statement more info	PubMed
involved_in eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in integrin biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of endodermal cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cellular component organization	IEA Inferred from Electronic Annotation more info
involved_in skin development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in supramolecular fiber organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tendon development	IEA Inferred from Electronic Annotation more info
involved_in wound healing, spreading of epidermal cells	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
part_of collagen type V trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type V trimer	IMP Inferred from Mutant Phenotype more info	PubMed
part_of collagen type V trimer	NAS Non-traceable Author Statement more info	PubMed
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	IMP Inferred from Mutant Phenotype more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-1(V) chain

Names: collagen, type V, alpha 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_008030.1 RefSeqGene

Range

5000..208038

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_737

mRNA and Protein(s)

NM_000093.5 → NP_000084.3 collagen alpha-1(V) chain isoform 1 preproprotein

See identical proteins and their annotated locations for NP_000084.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399221, CN399265, CN484933, ES314363

Consensus CDS

CCDS6982.1

UniProtKB/Swiss-Prot

A0A087WXW9, P20908, Q15094, Q5SUX4

UniProtKB/TrEMBL

B2ZZ86

Related

ENSP00000360882.3, ENST00000371817.8

Conserved Domains (3) summary

pfam01391
Location:871 → 930

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:39 → 230

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1610 → 1836

COLFI; Fibrillar collagen C-terminal domain
NM_001278074.1 → NP_001265003.1 collagen alpha-1(V) chain isoform 2 preproprotein

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2 which is of the same length but contains an alternate segment, compared to isoform 1. This variant is based on experimental data in PMID 22149965 and is supported by partial transcripts and RNA-seq data.

Source sequence(s)

AB209864, AB371583, AI190929, AL591890, BC032405, BM051019, CA446007, CB152831, CN399198, CN399221, CN399265, CN484933, ES314363

Consensus CDS

CCDS75932.1

UniProtKB/TrEMBL

B2ZZ86

Related

ENSP00000360885.4, ENST00000371820.4

Conserved Domains (3) summary

pfam01391
Location:871 → 930

Collagen; Collagen triple helix repeat (20 copies)

smart00210
Location:39 → 230

TSPN; Thrombospondin N-terminal -like domains

pfam01410
Location:1610 → 1836

COLFI; Fibrillar collagen C-terminal domain