COL6A2 collagen type VI alpha 2 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL6A2provided by HGNC
Official Full Name: collagen type VI alpha 2 chainprovided by HGNC
Primary source: HGNC:HGNC:2212
See related: Ensembl:ENSG00000142173 MIM:120240; AllianceGenome:HGNC:2212
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: UCMD1; BTHLM1; PP3610; UCMD1B; BTHLM1B
Summary: This gene encodes one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The product of this gene contains several domains similar to von Willebrand Factor type A domains. These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance of this collagen in organizing matrix components. Mutations in this gene are associated with Bethlem myopathy and Ullrich scleroatonic muscular dystrophy. Three transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in placenta (RPKM 164.0), endometrium (RPKM 155.3) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q22.3

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (46098112..46132848)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (44476193..44510935)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (47518026..47552762)

Chromosome 21 - NC_000021.9 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
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?

Extracellular Matrix Disorganization and Sarcolemmal Alterations in COL6-Related Myopathy Patients with New Variants of COL6 Genes.
Title: Extracellular Matrix Disorganization and Sarcolemmal Alterations in COL6-Related Myopathy Patients with New Variants of COL6 Genes.
Role of COL6A2 in malignant progression and temozolomide resistance of glioma.
Title: Role of COL6A2 in malignant progression and temozolomide resistance of glioma.
The Presentation of Two Unrelated Clinical Cases from the Republic of North Ossetia-Alania with the Same Previously Undescribed Variant in the COL6A2 Gene.
Title: The Presentation of Two Unrelated Clinical Cases from the Republic of North Ossetia-Alania with the Same Previously Undescribed Variant in the COL6A2 Gene.
Collagen type VIalpha1 and 2 repress the proliferation, migration and invasion of bladder cancer cells.
Title: Collagen type VI‑α1 and 2 repress the proliferation, migration and invasion of bladder cancer cells.
Use of RNAsequencing to detect abnormal transcription of the collagen alpha2 (VI) chain gene that can lead to Bethlem myopathy.
Title: Use of RNA‑sequencing to detect abnormal transcription of the collagen α‑2 (VI) chain gene that can lead to Bethlem myopathy.
Tendon Extracellular Matrix Remodeling and Defective Cell Polarization in the Presence of Collagen VI Mutations.
Title: Tendon Extracellular Matrix Remodeling and Defective Cell Polarization in the Presence of Collagen VI Mutations.
Proteomics Profiling Reveals Insulin-Like Growth Factor 1, Collagen Type VI alpha-2 Chain, and Fermitin Family Homolog 3 as Potential Biomarkers of Plaque Erosion in ST-Segment Elevated Myocardial Infarction.
Title: Proteomics Profiling Reveals Insulin-Like Growth Factor 1, Collagen Type VI α-2 Chain, and Fermitin Family Homolog 3 as Potential Biomarkers of Plaque Erosion in ST-Segment Elevated Myocardial Infarction.
binding of collagen VI to NG2 is essential for the direction of tendon fibroblasts migration in vitro.
Title: Collagen VI-NG2 axis in human tendon fibroblasts under conditions mimicking injury response.
Genetic study showed a missense mutation in COL6A2 (c.820 G>A, p.Gly268Ser) that causes a glycine substitution in the Gly-X-Y collagenous motif, at the beginning of the collagenous triple helical domain. The c.820 G>A mutation segregated in all the affected patients.
Title: Keloids, Spontaneous or After Minor Skin Injury: Importance of Not Missing Bethlem Myopathy.
Parental mosaicism was confirmed in the four families through quantitative analysis of the ratio of mutant versus wild-type allele (COL6A1, COL6A2, and COL6A3) in genomic DNA from various tissues; consistent with somatic mosaicism, parental samples had lower ratios of mutant versus wild-type allele compared with the fully heterozygote offspring.
Title: Mosaicism for dominant collagen 6 mutations as a cause for intrafamilial phenotypic variability.

Submit: New GeneRIF Correction See all GeneRIFs (30)

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
Bethlem myopathy 1B MedGen: CN376902 OMIM: 620725 GeneReviews: Collagen VI-Related Dystrophies	not available
Myosclerosis MedGen: C1850671 OMIM: 255600 GeneReviews: Collagen VI-Related Dystrophies	Compare labs
Ullrich congenital muscular dystrophy 1B MedGen: CN376896 OMIM: 620727 GeneReviews: Collagen VI-Related Dystrophies	not available

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

GDB:185152 (e-PCR)
- UniSTS:155410

GDB:192315 (e-PCR)
- UniSTS:155709

PMC34700P1 (e-PCR)
- UniSTS:273231

PMC34700P2 (e-PCR)
- UniSTS:273232

PMC34700P3 (e-PCR)
- UniSTS:273233

COL6A2_4061 (e-PCR)
- UniSTS:464472

RH80325 (e-PCR)
- UniSTS:90013

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables collagen binding	IPI Inferred from Physical Interaction more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	PubMed
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

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA Inferred from Electronic Annotation more info
involved_in response to UV	IEA Inferred from Electronic Annotation more info
involved_in response to glucose	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
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 extracellular exosome	HDA more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
located_in extracellular vesicle	HDA more info	PubMed
part_of protein-containing complex	IPI Inferred from Physical Interaction more info	PubMed
located_in sarcolemma	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-2(VI) chain

Names: collagen VI, alpha-2 polypeptide; collagen, type VI, alpha 2; epididymis secretory sperm binding protein; human mRNA for collagen VI alpha-2 C-terminal globular domain

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_008675.1 RefSeqGene

Range

5001..39731

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_476

mRNA and Protein(s)

NM_001849.4 → NP_001840.3 collagen alpha-2(VI) chain isoform 2C2 precursor

See identical proteins and their annotated locations for NP_001840.3

Status: REVIEWED

Description

Transcript Variant: This variant (2C2), that differs from the other variants in the last exon, encodes the full-length protein.

Source sequence(s)

AP001471, AY029208, BC065509, CN352095, CN352155

Consensus CDS

CCDS13728.1

UniProtKB/Swiss-Prot

P12110, Q13909, Q13910, Q13911, Q14048, Q14049, Q16259, Q16597, Q6P0Q1, Q9UML3, Q9Y4S8

UniProtKB/TrEMBL

A0A384MDP3

Related

ENSP00000300527.4, ENST00000300527.9

Conserved Domains (3) summary

pfam01391
Location:439 → 498

Collagen; Collagen triple helix repeat (20 copies)

cd01480
Location:612 → 803

vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: 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 ...

pfam00092
Location:833 → 1007

VWA; von Willebrand factor type A domain
NM_058174.3 → NP_478054.2 collagen alpha-2(VI) chain isoform 2C2a precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2C2a) has a different last exon than the other variants. Isoform 2C2a is 101 amino acids shorter than isoform 2C2 and 91 amino acids longer than isoform 2C2a'.

Source sequence(s)

AI275476, AP001471, BC065509, BM989656, CN352095, CN352155, X15977

Consensus CDS

CCDS13729.1

UniProtKB/Swiss-Prot

P12110

Related

ENSP00000380870.1, ENST00000397763.6

Conserved Domains (2) summary

pfam01391
Location:439 → 498

Collagen; Collagen triple helix repeat (20 copies)

cd01480
Location:612 → 803

vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: 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 ...
NM_058175.3 → NP_478055.2 collagen alpha-2(VI) chain isoform 2C2a' precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2C2a') encodes the shortest polypeptide. The last exon in this variant results in the use of a stop codon that shortens the protein by 192 amino acids compared to the full-length protein, although the transcripts are nearly the same length.

Source sequence(s)

AI275476, AP001471, BC065509, BM989656, CN352095, CN352155, M34570

Consensus CDS

CCDS13730.1

UniProtKB/Swiss-Prot

P12110

Related

ENSP00000387115.1, ENST00000409416.6

Conserved Domains (2) summary

pfam01391
Location:439 → 498

Collagen; Collagen triple helix repeat (20 copies)

cd01480
Location:612 → 803

vWA_collagen_alpha_1-VI-type; VWA_collagen alpha(VI) type: 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 ...