COL5A2

protein-coding

collagen type V alpha 2 chain, the group of Collagens|MicroRNA protein coding host genes

Gene 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. Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. [provided by RefSeq, Jul 2008]

MANE transcript

NM_000393.5

Inheritance

AD

ClinVar variants

P:70U:874B:683

Top phenotype

Ehlers-Danlos syndrome, classic type, 2

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr2:189,031,898-189,225,312

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~193.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Ehlers-Danlos syndrome, classic type, 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0019568

Submitter: Labcorp Genetics (formerly Invitae)

Ehlers-Danlos syndrome, classic type, 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0019568

Submitter: Genomics England PanelApp

Ehlers-Danlos syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0020066

Submitter: G2P

Ehlers-Danlos syndrome, classic typeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007522

Submitter: ClinGen

COL5A2 was first reported in relation to autosomal dominant Ehlers-Danlos syndrome (EDS), classic type, in 1998 (Michalickova et al, PMID: 9425231; Richards et al, PMID: 9783710). First described by Beighton in 1968, classic EDS (formerly known as EDS type I or “gravis” and type II or “mitis”) is a connective tissue disorder characterized by joint hypermobility, skin hyperextensibilty, and skin fragility leading to atrophic scarring (reviewed in Bowen et al, 2017, PMID: 28192633; Malfait et al, 2018, PMID 20301422). This curation includes nineteen unique variants (splicing variants causing in frame deletions, missense variants, one in frame deletion/insertion, and a 3’ terminal frameshift not expected to undergo nonsense-mediated decay) that have been reported in nineteen probands meeting clinical criteria for classic EDS in six publications (Michalickova et al, 1998, PMID: 9425231; Richards et al, 1998, PMID: 9783710; Malfait et al, 2005, PMID: 15580559; Symoens et al, 2012, PMID: 22696272; Ritelli et al, 2013, PMID: 23587214, Watanabe et al, 2016, PMID: 27656288). Of note, none of these variants is predicted to result in lack of protein. Like the other fibrillar collagens, alpha2(V) has a long uninterrupted triple helix of Gly-X-Y repeats. The glycine residues have been shown to be important to the triple helix structure (Long et al, 1993, PMID 8218237; Bella et al, 1994, PMID 7695699; Shoulders and Raines, 2009, PMID 19344236). Ten of the variants curated here cause in frame deletion of 18-36 amino acids in the helical domain, and one is an in frame insertion/deletion. With the exception of one frameshift in the 3’ end of the gene, all of the other variants curated involved missense substitutions of a glycine residue in the helical domain. Alteration or loss of the Gly-X-Y repeats in the helical region is expected to result in a dominant-negative mechanism of disease, with up to 50% of Collagen V chains incorporating an altered alpha2(V) chain. The relationship between COL5A2 and classic EDS is also supported by experimental evidence. This includes the biochemical function of COL5A2 in regulating collagen fiber size in the extra-cellular matrix, which is consistent with the clinical features of the condition (Andrikopoulos et al., 1995, PMID: 7704020; Fichard et al, 1995, PMID: 8535602; the interaction of the gene product of COL5A2 (alpha2(V)) in a triple helical structure with the gene product of COL5A1 (alpha1(V), another gene with a definitive relationship with classic EDS (Bentz H, et al., 1978, PMID: 738278); functional alteration evidence in which fibroblasts and dermis samples from a patient with classic EDS and a COL5A2 variant show abnormalities in collagen solubility and collagen fibril size (Michalickova et al, 1998, PMID: 9425231); the clinical features of animal models including a cow model with skin abnormalities and a COL5A2 variant (Jacinto et al, 2020, PMID: 33143196), a conditional mouse knockout with fragile skin and poor wound-healing (Park et al, 2017, PMID: 28734943), and mouse model with an in frame deletion of the N-telopeptide domain in which homozygotes have fragile, hyperextensible skin (Andrikopoulos et al, 1995, PMID: 7704020). In summary, COL5A2 is definitively associated with autosomal dominant classic EDS. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This gene-disease classification was approved by the General Gene Curation Expert panel on March 24th, 2021.

Ehlers-Danlos syndrome, classic typeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007522

Submitter: Orphanet

Clinical Genomic Database (CGD)

Ehlers-Danlos syndrome, classic type, 2AD

Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Dermatologic; Musculoskeletal; Obstetric; Ophthalmologic

Intervention: Cardiovascular; Obstetric

Rationale: Individuals may have aortic root dilatation, but the natural history is unclear, and may not typically progress, though yearly surveillance with echocardiogram when aortic dilatation or mitral valve prolapse is peresent has been recommended; Precautions in pregnancy may be beneficial

Refs: 9425231; 9783710; 12180144; 16278879; 15580559; 20301422; 20847697Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COL5A2 variants in ClinVar

26 Conditions Cataloged
Ehlers-Danlos syndrome, classic type, 1Total: 1673
not providedTotal: 644
Familial thoracic aortic aneurysm and aortic dissectionTotal: 614
not specifiedTotal: 420
Ehlers-Danlos syndrome, classic type, 2Total: 201
COL5A2-related disorderTotal: 86
Ehlers-Danlos syndromeTotal: 51
Ehlers-Danlos syndrome, classic typeTotal: 47

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000393.5. 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
1
clinvar
2
clinvar
19
clinvar
445
clinvar
9
clinvar
476
missense
3
clinvar
29
clinvar
819
clinvar
219
clinvar
10
clinvar
1080
nonsense
3
clinvar
6
clinvar
9
start loss
1
clinvar
1
frameshift
5
clinvar
4
clinvar
6
clinvar
15
splice donor/acceptor (+/-2bp)
7
clinvar
16
clinvar
23
clinvar
46
Total1951874664191627

Highest pathogenic variant AF is 0.000047903446

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000393.5RefSeqNP_000384.254MANE Select
ENST00000374866.9EnsemblENSP00000364000.354MANE Select
ENST00000618828.1EnsemblENSP00000482184.140Standard
ENST00000618828.2EnsemblENSP00000482184.140Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Protein digestion and absorption - Homo sapiens (human)
  • miRNA targets in ECM and membrane receptors
  • Focal Adhesion
  • Focal Adhesion-PI3K-Akt-mTOR-signaling pathway
  • Collagen chain trimerization

Biological Process

  • skeletal system development
  • ossification
  • extracellular matrix organization
  • collagen fibril organization
  • notochord development

Molecular Function

  • extracellular matrix structural constituent
  • extracellular matrix structural constituent conferring tensile strength
  • SMAD binding
  • metal ion binding

Cellular Component

  • extracellular region
  • collagen trimer
  • collagen type V trimer
  • extracellular space
  • endoplasmic reticulum lumen

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000374866
Coding exons
54
Length
147984
Individuals with no LoFs
125725
Homozygous LoFs
0
Heterozygous LoFs
21
Defined
125746
p
0.0000835
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.446798830.7690.00004849373
Missense (PolyPhen)165259.940.634752644
Synonymous0.1602732760.9880.00001513279
Loss of Function8.63494.50.04230.000005131113

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.000370.00037rare
European (Non-Finnish)0.0000970.000097rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin. Type V collagen is a key determinant in the assembly of tissue- specific matrices (By similarity). {ECO:0000250}.;
Disease
DISEASE: Ehlers-Danlos syndrome, classic type, 2 (EDSCL2) [MIM:130010]: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. The main features of classic Ehlers-Danlos syndrome are joint hypermobility and dislocation, and fragile, bruisable skin. EDSCL2 inheritance is autosomal dominant. {ECO:0000269|PubMed:27656288, ECO:0000269|PubMed:9425231, ECO:0000269|PubMed:9783710}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.391

Intolerance Scores

LoFtool
0.00489
RVIS EVS
-0.87
RVIS percentile EVS
10.59

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.331

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.