COL6A1 collagen type VI alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL6A1provided by HGNC
Official Full Name: collagen type VI alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:2211
See related: Ensembl:ENSG00000142156 MIM:120220; AllianceGenome:HGNC:2211
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: OPLL; BTHLM1; UCHMD1; BTHLM1A; UCHMD1A
Summary: The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues. Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element. Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the autosomal dominant disorder, Bethlem myopathy. [provided by RefSeq, Jul 2008]
Expression: Broad expression in placenta (RPKM 211.0), endometrium (RPKM 191.1) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q22.3

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (45981770..46005048)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (44356236..44380470)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (47401684..47424962)

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 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?

Exome sequencing in extreme altitude mountaineers identifies pathogenic variants in RTEL1 and COL6A1 previously associated with respiratory failure.
Title: Exome sequencing in extreme altitude mountaineers identifies pathogenic variants in RTEL1 and COL6A1 previously associated with respiratory failure.
Homozygous splice variant (c.1741-6G>A) of the COL6A1 gene in three patients with Ullrich congenital muscular dystrophy.
Title: Homozygous splice variant (c.1741-6G>A) of the COL6A1 gene in three patients with Ullrich congenital muscular dystrophy.
Integrated Proteomics and Metabolomics Analyses of Serum in Chinese Patients with Severe and Active Graves' Orbitopathy: A Cross-sectional Study.
Title: Integrated Proteomics and Metabolomics Analyses of Serum in Chinese Patients with Severe and Active Graves' Orbitopathy: A Cross-sectional Study.
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.
Intrafamilial Phenotypic Variability of Collagen VI-Related Myopathy Due to a New Mutation in the COL6A1 Gene.
Title: Intrafamilial Phenotypic Variability of Collagen VI-Related Myopathy Due to a New Mutation in the COL6A1 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.
Identification of COL6A1 as the Key Gene Associated with Antivascular Endothelial Growth Factor Therapy in Glioblastoma Multiforme.
Title: Identification of COL6A1 as the Key Gene Associated with Antivascular Endothelial Growth Factor Therapy in Glioblastoma Multiforme.
Association analysis and functional study of COL6A1 single nucleotide polymorphisms in thoracic ossification of the ligamentum flavum in the Chinese Han population.
Title: Association analysis and functional study of COL6A1 single nucleotide polymorphisms in thoracic ossification of the ligamentum flavum in the Chinese Han population.
Non-canonical Fzd7 signaling contributes to breast cancer mesenchymal-like stemness involving Col6a1.
Title: Non-canonical Fzd7 signaling contributes to breast cancer mesenchymal-like stemness involving Col6a1.
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.

Submit: New GeneRIF Correction See all GeneRIFs (73)

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 1A MedGen: CN029274 OMIM: 158810 GeneReviews: Collagen VI-Related Dystrophies	not available
Collagen 6-related myopathy MedGen: CN117976 GeneReviews: Collagen VI-Related Dystrophies	not available
Ullrich congenital muscular dystrophy 1A MedGen: C0410179 OMIM: 254090 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

RH75955 (e-PCR)
- UniSTS:88836

STS_CEB250 (e-PCR)
- UniSTS:255254

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	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 platelet-derived growth factor binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in 2-oxoglutarate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in adipose tissue development	IEA Inferred from Electronic Annotation more info
involved_in apoptotic nuclear changes	IEA Inferred from Electronic Annotation more info
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in basement membrane organization	IEA Inferred from Electronic Annotation more info
involved_in bone development	IEA Inferred from Electronic Annotation more info
involved_in bone mineralization	IEA Inferred from Electronic Annotation more info
involved_in canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cartilage development	IEA Inferred from Electronic Annotation more info
involved_in caveola assembly	IEA Inferred from Electronic Annotation more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
involved_in circadian rhythm	IEA Inferred from Electronic Annotation more info
involved_in collagen fibril organization	IEA Inferred from Electronic Annotation more info
involved_in collagen metabolic process	IEA Inferred from Electronic Annotation more info
involved_in endodermal cell differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in energy reserve metabolic process	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix assembly	IEA Inferred from Electronic Annotation more info
involved_in fat cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in glycolytic process	IEA Inferred from Electronic Annotation more info
involved_in hair follicle development	IEA Inferred from Electronic Annotation more info
involved_in heart development	IEA Inferred from Electronic Annotation more info
involved_in homeostasis of number of cells	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in insulin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in insulin-like growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in limb joint morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in lung alveolus development	IEA Inferred from Electronic Annotation more info
involved_in lung epithelial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in lung morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial depolarization	IEA Inferred from Electronic Annotation more info
involved_in mitochondrial transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion organization	IEA Inferred from Electronic Annotation more info
involved_in multicellular organismal locomotion	IEA Inferred from Electronic Annotation more info
involved_in muscle cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in muscle system process	IEA Inferred from Electronic Annotation more info
involved_in myelination in peripheral nervous system	IEA Inferred from Electronic Annotation more info
involved_in neuron apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	HDA more info	PubMed
involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA Inferred from Electronic Annotation more info
involved_in protein tetramerization	IEA Inferred from Electronic Annotation more info
involved_in reactive oxygen species metabolic process	IEA Inferred from Electronic Annotation more info
involved_in reduction of food intake in response to dietary excess	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell size	IEA Inferred from Electronic Annotation more info
involved_in regulation of collagen fibril organization	IEA Inferred from Electronic Annotation more info
involved_in respiratory system process	IEA Inferred from Electronic Annotation more info
involved_in response to UV	IEA Inferred from Electronic Annotation more info
involved_in response to bleomycin	IEA Inferred from Electronic Annotation more info
involved_in response to decreased oxygen levels	IEA Inferred from Electronic Annotation more info
involved_in response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in response to mechanical stimulus	IEA Inferred from Electronic Annotation more info
involved_in response to muscle activity	IEA Inferred from Electronic Annotation more info
involved_in response to pain	IEA Inferred from Electronic Annotation more info
involved_in response to peptide	IEA Inferred from Electronic Annotation more info
involved_in response to polyamine macromolecule	IEA Inferred from Electronic Annotation more info
involved_in response to reactive oxygen species	IEA Inferred from Electronic Annotation more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info
involved_in response to wounding	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of mechanical stimulus	IEA Inferred from Electronic Annotation more info
involved_in single fertilization	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle fiber development	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle fiber differentiation	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle tissue growth	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle tissue regeneration	IEA Inferred from Electronic Annotation more info
involved_in tissue remodeling	IEA Inferred from Electronic Annotation more info
involved_in transmission of nerve impulse	IEA Inferred from Electronic Annotation more info
involved_in tricarboxylic acid cycle	IEA Inferred from Electronic Annotation more info
involved_in uterus development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
part_of collagen type VI 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
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 intracellular vesicle	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in myofibril	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IPI Inferred from Physical Interaction more info	PubMed
located_in sarcolemma	IEA Inferred from Electronic Annotation more info
located_in sarcoplasmic reticulum	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagen alpha-1(VI) chain

Names: alpha 1 (VI) chain (61 AA); collagen VI, alpha-1 polypeptide; collagen, type VI, alpha 1; 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_008674.1 RefSeqGene

Range

5001..28301

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_475

mRNA and Protein(s)

NM_001848.3 → NP_001839.2 collagen alpha-1(VI) chain precursor

See identical proteins and their annotated locations for NP_001839.2

Status: REVIEWED

Source sequence(s)

AU100220, BC052575, BI769554, BM686857, BM707144, CN369002, CN369026, CN369041

Consensus CDS

CCDS13727.1

UniProtKB/Swiss-Prot

O00117, O00118, P12109, Q14040, Q14041, Q16258, Q7Z645, Q9BSA8

UniProtKB/TrEMBL

A0A384P5H7

Related

ENSP00000355180.3, ENST00000361866.8

Conserved Domains (3) summary

PHA03169
Location:368 → 520

PHA03169; hypothetical protein; Provisional

cd01480
Location:34 → 227

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 ...

pfam01391
Location:256 → 309

Collagen; Collagen triple helix repeat (20 copies)