COL6A3 collagen type VI alpha 3 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL6A3provided by HGNC
Official Full Name: collagen type VI alpha 3 chainprovided by HGNC
Primary source: HGNC:HGNC:2213
See related: Ensembl:ENSG00000163359 MIM:120250; AllianceGenome:HGNC:2213
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: DYT27; UCMD1; BTHLM1; UCMD1C; BTHLM1C
Summary: This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2 chains. This difference in size is largely due to an increase in the number of subdomains, similar to von Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains. 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 the type VI collagen genes are associated with Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple transcript variants have been identified, but the full-length nature of only some of these variants has been described. [provided by RefSeq, Jun 2009]
Expression: Broad expression in gall bladder (RPKM 140.2), endometrium (RPKM 95.0) and 16 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.3

Exon count:: 44

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (237324018..237414164, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (237815093..237905193, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (238232661..238322807, complement)

Chromosome 2 - NC_000002.12 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
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?

Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence.
Title: Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence.
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.
Genetic Analysis of HIBM Myopathy-Specific GNE V727M Hotspot Mutation Identifies a Novel COL6A3 Allied Gene Signature That Is Also Deregulated in Multiple Neuromuscular Diseases and Myopathies.
Title: Genetic Analysis of HIBM Myopathy-Specific GNE V727M Hotspot Mutation Identifies a Novel COL6A3 Allied Gene Signature That Is Also Deregulated in Multiple Neuromuscular Diseases and Myopathies.
Clinical and Molecular Spectrum Associated with COL6A3 c.7447A>G p.(Lys2483Glu) Variant: Elucidating its Role in Collagen VI-related Myopathies.
Title: Clinical and Molecular Spectrum Associated with COL6A3 c.7447A>G p.(Lys2483Glu) Variant: Elucidating its Role in Collagen VI-related Myopathies.
Collagen VI-related limb-girdle syndrome caused by frequent mutation in COL6A3 gene with conflicting reports of pathogenicity.
Title: Collagen VI-related limb-girdle syndrome caused by frequent mutation in COL6A3 gene with conflicting reports of pathogenicity.
Coexistence of digenic mutations in the collagen VI genes (COL6A1 and COL6A3) leads to Bethlem myopathy.
Title: Coexistence of digenic mutations in the collagen VI genes (COL6A1 and COL6A3) leads to Bethlem myopathy.
Identification of Key Prognostic Biomarker and Its Correlation with Immune Infiltrates in Pancreatic Ductal Adenocarcinoma.
Title: Identification of Key Prognostic Biomarker and Its Correlation with Immune Infiltrates in Pancreatic Ductal Adenocarcinoma.
Study of the collagen type VI alpha 3 (COL6A3) gene in Parkinson's disease.
Title: Study of the collagen type VI alpha 3 (COL6A3) gene in Parkinson's disease.
COL6A3 expression in adipose tissue cells is associated with levels of the homeobox transcription factor PRRX1.
Title: COL6A3 expression in adipose tissue cells is associated with levels of the homeobox transcription factor PRRX1.
Structure of a collagen VI alpha3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations.
Title: Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations.

Submit: New GeneRIF Correction See all GeneRIFs (52)

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 1C MedGen: CN376903 OMIM: 620726 GeneReviews: Collagen VI-Related Dystrophies	not available
Dystonia 27 MedGen: C4225336 OMIM: 616411 GeneReviews: Not available	Compare labs
Ullrich congenital muscular dystrophy 1C MedGen: CN376897 OMIM: 620728 GeneReviews: Collagen VI-Related Dystrophies	not available

EBI GWAS Catalog

Description
A genome-wide association study of aging. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

COL6A3_1840 (e-PCR)
- UniSTS:280619

G38154 (e-PCR)
- UniSTS:53341

D10S16 (e-PCR)
- UniSTS:155756

G44334 (e-PCR)
- UniSTS:95121

WI-19458 (e-PCR)
- UniSTS:68797

RH18099 (e-PCR)
- UniSTS:4294

Clone Names

FLJ34702, FLJ98399, DKFZp686N0262, DKFZp686D23123, DKFZp686K04147

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 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 muscle organ development	TAS Traceable Author Statement more info	PubMed
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 type VI trimer	TAS 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
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 matrix	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	HDA more info	PubMed
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
located_in extracellular vesicle	HDA more info	PubMed
located_in sarcolemma	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-3(VI) chain

Names: collagen VI, alpha-3 polypeptide; collagen, type VI, alpha 3; epididymis secretory sperm binding protein

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_008676.1 RefSeqGene

Range

5001..95196

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_473

mRNA and Protein(s)

NM_004369.4 → NP_004360.2 collagen alpha-3(VI) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_004360.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the full-length isoform (1).

Source sequence(s)

AK092021, AK308451, BC033174, BU687672, BX647500, X52022

Consensus CDS

CCDS33412.1

UniProtKB/Swiss-Prot

A8MT30, B4E3U5, B7ZMJ7, E9PFQ6, E9PGQ9, P12111, Q16501, Q53QF4, Q53QF6

UniProtKB/TrEMBL

D9ZGF2

Related

ENSP00000295550.4, ENST00000295550.9

Conserved Domains (7) summary

pfam01391
Location:2314 → 2371

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:2993 → 3061

FN3; Fibronectin type 3 domain

smart00327
Location:1838 → 1994

VWA; von Willebrand factor (vWF) type A domain

cd01481
Location:1435 → 1599

vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...

pfam00014
Location:3111 → 3162

Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain

pfam00092
Location:1639 → 1811

VWA; von Willebrand factor type A domain

cl00057
Location:1028 → 1191

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_057164.5 → NP_476505.3 collagen alpha-3(VI) chain isoform 2 precursor

See identical proteins and their annotated locations for NP_476505.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 5' coding region, lacks several exons in the 3' coding region, but contains an alternate 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is significantly shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK092021, BX647500, DC411101

Consensus CDS

CCDS54439.1

UniProtKB/TrEMBL

Q63HQ4

Related

ENSP00000375860.2, ENST00000392003.6

Conserved Domains (2) summary

cd01481
Location:37 → 201

vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...

cl00057
Location:621 → 784

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_057165.5 → NP_476506.3 collagen alpha-3(VI) chain isoform 3 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, lacks several exons in the 3' coding region, but contains an alternate 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) is significantly shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK304870, BX647500

Consensus CDS

CCDS33411.2

UniProtKB/TrEMBL

Q63HQ4

Related

ENSP00000375861.3, ENST00000392004.7

Conserved Domains (2) summary

cd01481
Location:238 → 402

vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...

cl00057
Location:822 → 985

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_057166.5 → NP_476507.3 collagen alpha-3(VI) chain isoform 4 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks three alternate in-frame exons in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.

Source sequence(s)

BC144595, BC171790, BU687672, DC411101

Consensus CDS

CCDS33410.2

UniProtKB/TrEMBL

B7ZW00

Related

ENSP00000418285.1, ENST00000472056.5

Conserved Domains (7) summary

pfam01391
Location:1707 → 1764

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:2386 → 2454

FN3; Fibronectin type 3 domain

smart00327
Location:1231 → 1387

VWA; von Willebrand factor (vWF) type A domain

cd01481
Location:828 → 992

vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...

pfam00014
Location:2504 → 2555

Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain

pfam00092
Location:1032 → 1204

VWA; von Willebrand factor type A domain

cl00057
Location:421 → 584

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
NM_057167.4 → NP_476508.2 collagen alpha-3(VI) chain isoform 5 precursor

See identical proteins and their annotated locations for NP_476508.2

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (5) that is shorter than isoform 1.

Source sequence(s)

AK092021, AK308451, BC033174, BU687672, BX647500, DC411101, X52022

Consensus CDS

CCDS33409.1

UniProtKB/TrEMBL

B7ZW00

Related

ENSP00000315873.4, ENST00000353578.9

Conserved Domains (7) summary

pfam01391
Location:2108 → 2165

Collagen; Collagen triple helix repeat (20 copies)

smart00060
Location:2787 → 2855

FN3; Fibronectin type 3 domain

smart00327
Location:1632 → 1788

VWA; von Willebrand factor (vWF) type A domain

cd01481
Location:1229 → 1393

vWA_collagen_alpha3-VI-like; VWA_collagen alpha 3(VI) like: 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 ...

pfam00014
Location:2905 → 2956

Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain

pfam00092
Location:1433 → 1605

VWA; von Willebrand factor type A domain

cl00057
Location:822 → 985

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...