COL6A5 collagen type VI alpha 5 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL6A5provided by HGNC
Official Full Name: collagen type VI alpha 5 chainprovided by HGNC
Primary source: HGNC:HGNC:26674
See related: Ensembl:ENSG00000172752 MIM:611916; AllianceGenome:HGNC:26674
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: VWA4; COL29A1
Summary: This gene encodes a member of the collagen superfamily of proteins. The encoded protein contains multiple von Willebrand factor A-like domains and may interact with the alpha 1 and alpha 2 chains of collagen VI to form the complete collagen VI trimer. Polymorphisms in this gene may be linked to dermal phenotypes, such as eczema. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]
Expression: Biased expression in skin (RPKM 1.9), lung (RPKM 1.6) and 8 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q22.1

Exon count:: 42

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (130345672..130484846)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (133089679..133228818)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (130064515..130203690)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1.
Title: Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1.
RNAseq-Based Prioritization Revealed COL6A5, COL8A1, COL10A1 and MIR146A as Common and Differential Susceptibility Biomarkers for Psoriasis and Psoriatic Arthritis: Confirmation from Genotyping Analysis of 1417 Italian Subjects.
Title: RNAseq-Based Prioritization Revealed COL6A5, COL8A1, COL10A1 and MIR146A as Common and Differential Susceptibility Biomarkers for Psoriasis and Psoriatic Arthritis: Confirmation from Genotyping Analysis of 1417 Italian Subjects.
Collagen type VI alpha5 gene variations may predict the risk of lung cancer development in Chinese Han population.
Title: Collagen type VI α5 gene variations may predict the risk of lung cancer development in Chinese Han population.
three polymorphisms located in COL6A5, COL8A1, and COL10A1 were investigated as potential susceptibility biomarkers for atopic eczema.
Title: Atopic Eczema: Genetic Analysis of COL6A5, COL8A1, and COL10A1 in Mediterranean Populations.
The longitudinal EWAS for the recessive model showed that a novel SNV, rs11917356 of COL6A5, was significantly associated with systolic blood pressure, and the derived allele at the SNV may have spread throughout East Asia in recent evolutionary time.
Title: Longitudinal exome-wide association study to identify genetic susceptibility loci for hypertension in a Japanese population.
This study demonstrated that an association between COL6A5 gene and familiar chronic itch, suggesting a new contributor to the pathogenesis of neuropathic itch.
Title: COL6A5 variants in familial neuropathic chronic itch.
The collagen VI alpha5 chain is selectively localized at the basement membrane of myotendinous junctions.
Title: Expression of collagen VI α5 and α6 chains in human muscle and in Duchenne muscular dystrophy-related muscle fibrosis.
Our results suggest that COL29A1 is unlikely to contain genetic variants that have a major effect on eczema or atopy susceptibility.
Title: A comprehensive analysis of the COL29A1 gene does not support a role in eczema.
localization of alpha5, and to a lesser extent alpha6, is restricted to the papillary dermis, where the protein mainly colocalizes with collagen fibrils; both chains were found around blood vessels
Title: Expression of the collagen VI α5 and α6 chains in normal human skin and in skin of patients with collagen VI-related myopathies.
The role of the COL29A1 gene as an atopic dermatitis gene was not supported. Also, COL29A1 did not play a substantial role in the pathogenesis of chronic obstructive pulmonary disease or asthma.
Title: Variation in the COL29A1 gene in German patients with atopic dermatitis, asthma and chronic obstructive pulmonary disease.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2021-02-02) ClinGen Genome Curation Page Haploinsufficency Dosage sensitivity unlikely (Last evaluated 2021-02-02) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children. 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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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	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

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity 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

General protein information

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Preferred Names: collagen alpha-5(VI) chain

Names: collagen, type VI, alpha 5; collagen, type XXIX, alpha 1; von Willebrand factor A domain-containing protein 4

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_021424.2 RefSeqGene

Range

5002..144176

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001278298.2 → NP_001265227.1 collagen alpha-5(VI) chain isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the allele encoded by the GRCh38 reference genome and encodes isoform (1).

Source sequence(s)

AC093004, AC117398, KF573676

Consensus CDS

CCDS93384.1

UniProtKB/Swiss-Prot

A8TX70, A9J6L2, A9J6L4, A9J6L6, A9J6L7, A9J6M0, A9J6M1, A9J6M2, B5MEA7, Q6ZW26, Q8NA36

UniProtKB/TrEMBL

H0Y393

Related

ENSP00000362250.5, ENST00000373157.9

Conserved Domains (6) summary

pfam01391
Location:1564 → 1623

Collagen; Collagen triple helix repeat (20 copies)

COG2304
Location:445 → 593

YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]

cd01450
Location:2290 → 2467

vWFA_subfamily_ECM; 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 ...

cd01472
Location:627 → 787

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

pfam00092
Location:814 → 985

VWA; von Willebrand factor type A domain

cl00057
Location:29 → 195

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_001412157.1 → NP_001399086.1 collagen alpha-5(VI) chain isoform 3 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses the same exon combination as variant 1 but represents the allele encoded by the T2T-CHM13v2.0 genome assembly. The encoded isoform (3) has a frameshifted C-terminus compared to isoform 1.

Source sequence(s)

CP068275
NM_153264.7 → NP_694996.5 collagen alpha-5(VI) chain isoform 2 precursor

Status: REVIEWED

Source sequence(s)

AC093004, AC117398, KF573676

Consensus CDS

CCDS93385.1

UniProtKB/Swiss-Prot

A8TX70, A9J6L2, A9J6L4, A9J6L6, A9J6L7, A9J6M0, A9J6M1, A9J6M2, B5MEA7, Q6ZW26, Q8NA36

Related

ENSP00000422898.2, ENST00000512836.6

Conserved Domains (6) summary

cd01450
Location:2290 → 2467

vWFA_subfamily_ECM; 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 ...

cd01472
Location:627 → 787

vWA_collagen; von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form ...

pfam01391
Location:1394 → 1447

Collagen; Collagen triple helix repeat (20 copies)

pfam00092
Location:814 → 985

VWA; von Willebrand factor type A domain

NF038329
Location:1478 → 1730

gly_rich_SclB; LPXTG-anchored collagen-like adhesin Scl2/SclB

cl00057
Location:29 → 195

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 ...