COL6A5

gene
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Also known as FLJ35880VWA4

Summary

COL6A5 (collagen type VI alpha 5 chain, HGNC:26674) is a protein-coding gene on chromosome 3q22.1, encoding Collagen alpha-5(VI) chain (A8TX70). Collagen VI acts as a cell-binding protein.

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.

Source: NCBI Gene 256076 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 406 total
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency dosage sensitivity unlikely, triplosensitivity no evidence
  • MANE Select transcript: NM_001278298

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26674
Approved symbolCOL6A5
Namecollagen type VI alpha 5 chain
Location3q22.1
Locus typegene with protein product
StatusApproved
AliasesFLJ35880, VWA4
Ensembl geneENSG00000172752
Ensembl biotypeprotein_coding
OMIM611916
Entrez256076

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000312481, ENST00000373157, ENST00000512482, ENST00000512836

RefSeq mRNA: 3 — MANE Select: NM_001278298 NM_001278298, NM_001412157, NM_153264

CCDS: CCDS93384, CCDS93385

Canonical transcript exons

ENST00000373157 — 41 exons

ExonStartEnd
ENSE00001194266130470871130470967
ENSE00001194273130468795130469481
ENSE00001194278130455455130455666
ENSE00001194287130443476130443566
ENSE00001379257130440166130440825
ENSE00001531459130439522130439615
ENSE00001531461130431465130431949
ENSE00001547997130421325130421360
ENSE00001548142130409326130409388
ENSE00001548940130405993130406019
ENSE00001551288130401031130401173
ENSE00001552037130415645130415707
ENSE00001552649130398030130398111
ENSE00001553178130410009130410074
ENSE00001553245130416757130416819
ENSE00001553637130414069130414131
ENSE00001553744130418869130418931
ENSE00001553925130423838130423900
ENSE00001554307130373611130373705
ENSE00001555371130406131130406175
ENSE00001556081130405588130405659
ENSE00001557802130391179130391754
ENSE00001559014130426367130426403
ENSE00001559270130397583130397923
ENSE00001559767130403609130403662
ENSE00001560348130379418130380050
ENSE00001560961130422720130422782
ENSE00001561139130413545130413580
ENSE00001561816130410471130410524
ENSE00001562090130406268130406321
ENSE00001562324130376237130376836
ENSE00001562534130394890130395465
ENSE00001562755130401762130401854
ENSE00001563783130426214130426249
ENSE00001564067130388580130389134
ENSE00001564082130421153130421203
ENSE00001564320130384804130385364
ENSE00001634300130471682130471926
ENSE00002055710130484035130484846
ENSE00002421519130429573130429584
ENSE00003970013130345672130345981

Expression profiles

Bgee: expression breadth broad, 58 present calls, max score 86.11.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0560 / max 11.2069, expressed in 33 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
385800.056033

Top tissues by expression

227 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
upper leg skinUBERON:000426286.11gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047376.93gold quality
upper lobe of left lungUBERON:000895274.24gold quality
upper lobe of lungUBERON:000894873.38gold quality
skin of hipUBERON:000155470.21gold quality
lungUBERON:000204869.83gold quality
right lungUBERON:000216768.26gold quality
lower lobe of lungUBERON:000894967.51silver quality
duodenumUBERON:000211461.61gold quality
skin of abdomenUBERON:000141660.14gold quality
lower esophagus mucosaUBERON:003583459.35gold quality
visceral pleuraUBERON:000240158.72gold quality
colonic epitheliumUBERON:000039755.64gold quality
zone of skinUBERON:000001455.39gold quality
jejunal mucosaUBERON:000039955.09gold quality
cardia of stomachUBERON:000116253.77gold quality
esophagus mucosaUBERON:000246953.39gold quality
left testisUBERON:000453352.64gold quality
testisUBERON:000047351.83gold quality
urinary bladderUBERON:000125551.67gold quality
bone marrow cellCL:000209250.49gold quality
skin of legUBERON:000151150.40gold quality
right testisUBERON:000453449.53gold quality
vermiform appendixUBERON:000115449.44gold quality
fundus of stomachUBERON:000116049.36gold quality
caecumUBERON:000115348.57gold quality
jejunumUBERON:000211548.29gold quality
stomachUBERON:000094547.35gold quality
rectumUBERON:000105247.35gold quality
bone marrowUBERON:000237146.01silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

50 targeting COL6A5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4692100.0067.322066
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-428299.9975.366408
HSA-MIR-451499.9967.101870
HSA-MIR-4789-5P99.9870.762721
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-365899.9673.874379
HSA-MIR-545-3P99.9570.742783
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-4697-3P99.8967.091123
HSA-MIR-221-3P99.8671.561329
HSA-MIR-222-3P99.8671.351337
HSA-MIR-451699.6167.783390
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-143-3P99.4969.051457
HSA-MIR-477099.4969.091451
HSA-MIR-330-3P99.4169.952521
HSA-MIR-568399.3668.592083
HSA-MIR-608899.2968.451284
HSA-MIR-427999.1966.702437
HSA-MIR-443499.1067.011984
HSA-MIR-570399.1067.092053
HSA-MIR-7151-3P99.0469.722370

Functional genomics

ClinGen dosage: haploinsufficiency 40 (dosage sensitivity unlikely), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 13)

  • To identify the underlying atopic dermatitis disease gene, a dense map of microsatellite markers and single nucleotide polymorphisms was used, and association with AD was detected. (PMID:17850181)
  • The discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix. (PMID:18400749)
  • unlike eczema, genetic variation at COL29A1 and IL31 loci is unlikely to impact inflammatory bowel disease risk (PMID:18839421)
  • 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. (PMID:20649719)
  • 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 (PMID:20882040)
  • Our results suggest that COL29A1 is unlikely to contain genetic variants that have a major effect on eczema or atopy susceptibility. (PMID:21353297)
  • The collagen VI alpha5 chain is selectively localized at the basement membrane of myotendinous junctions. (PMID:22226732)
  • This study demonstrated that an association between COL6A5 gene and familiar chronic itch, suggesting a new contributor to the pathogenesis of neuropathic itch. (PMID:28073787)
  • 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. (PMID:29217820)
  • three polymorphisms located in COL6A5, COL8A1, and COL10A1 were investigated as potential susceptibility biomarkers for atopic eczema. (PMID:31275967)
  • Collagen type VI alpha5 gene variations may predict the risk of lung cancer development in Chinese Han population. (PMID:32193401)
  • 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. (PMID:32326527)
  • Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1. (PMID:33974636)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusCol6a5ENSMUSG00000091345
rattus_norvegicusCol6a5ENSRNOG00000010663
caenorhabditis_elegansWBGENE00003497
caenorhabditis_elegansWBGENE00007800

Paralogs (12): COCH (ENSG00000100473), COL12A1 (ENSG00000111799), MATN4 (ENSG00000124159), MATN3 (ENSG00000132031), MATN2 (ENSG00000132561), MATN1 (ENSG00000162510), COL6A3 (ENSG00000163359), VWA2 (ENSG00000165816), VWA1 (ENSG00000179403), COL14A1 (ENSG00000187955), VIT (ENSG00000205221), COL6A6 (ENSG00000206384)

Protein

Protein identifiers

Collagen alpha-5(VI) chainA8TX70 (reviewed: A8TX70)

Alternative names: Collagen alpha-1(XXIX) chain, von Willebrand factor A domain-containing protein 4

All UniProt accessions (4): A8TX70, H0Y393, H0Y935, H0Y9T2

UniProt curated annotations — full annotation on UniProt →

Function. Collagen VI acts as a cell-binding protein.

Subunit / interactions. Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) or alpha-6(VI).

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Expressed in skin, followed by lung, small intestine, colon and testis. In skin, it is expressed in the epidermis with strongest staining in suprabasal viable layers. In ATOD patients, it is absent in the most differentiated upper spinous and granular layers (at protein level).

Post-translational modifications. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.

Disease relevance. Patients affected by atopic dermatitis display an abnormal distribution of COL29A1 mRNA and protein in skin suggesting that COL29A1 may be involved in the pathogenesis of the disease.

Similarity. Belongs to the type VI collagen family.

Isoforms (2)

UniProt IDNamesCanonical?
A8TX70-11yes
A8TX70-22

RefSeq proteins (3): NP_001265227, NP_001399086, NP_694996 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002035VWF_ADomain
IPR008160CollagenRepeat
IPR036465vWFA_dom_sfHomologous_superfamily
IPR050525ECM_Assembly_OrgFamily

Pfam: PF00092, PF01391

UniProt features (46 total): domain 16, sequence variant 11, region of interest 4, glycosylation site 4, compositionally biased region 3, sequence conflict 3, splice variant 2, signal peptide 1, chain 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A8TX70-F170.940.17

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (4): 201, 260, 835, 2509

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-1442490Collagen degradation
R-HSA-1650814Collagen biosynthesis and modifying enzymes
R-HSA-186797Signaling by PDGF
R-HSA-2022090Assembly of collagen fibrils and other multimeric structures
R-HSA-216083Integrin cell surface interactions
R-HSA-3000178ECM proteoglycans
R-HSA-419037NCAM1 interactions
R-HSA-8948216Collagen chain trimerization

MSigDB gene sets: 66 (showing top): GOCC_COLLAGEN_TRIMER, REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, chr3q22, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS, GOCC_COMPLEX_OF_COLLAGEN_TRIMERS, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, REACTOME_SIGNALING_BY_PDGF, GOCC_SUPRAMOLECULAR_COMPLEX, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT_CONFERRING_TENSILE_STRENGTH, REACTOME_COLLAGEN_DEGRADATION, REACTOME_COLLAGEN_BIOSYNTHESIS_AND_MODIFYING_ENZYMES, REACTOME_ASSEMBLY_OF_COLLAGEN_FIBRILS_AND_OTHER_MULTIMERIC_STRUCTURES, REACTOME_ECM_PROTEOGLYCANS

GO Biological Process (2): cell adhesion (GO:0007155), extracellular matrix organization (GO:0030198)

GO Molecular Function (2): extracellular matrix structural constituent conferring tensile strength (GO:0030020), protein binding (GO:0005515)

GO Cellular Component (4): extracellular region (GO:0005576), collagen type VI trimer (GO:0005589), extracellular matrix (GO:0031012), collagen trimer (GO:0005581)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Collagen formation2
Extracellular matrix organization2
Degradation of the extracellular matrix1
Signaling by Receptor Tyrosine Kinases1
NCAM signaling for neurite out-growth1
Collagen biosynthesis and modifying enzymes1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular process1
extracellular structure organization1
external encapsulating structure organization1
extracellular matrix structural constituent1
binding1
cellular anatomical structure1
collagen beaded filament1
von-Willerbrand-factor-A-domain-rich collagen trimer1
extracellular protein-containing complex1
external encapsulating structure1
protein-containing complex1

Protein interactions and networks

STRING

1080 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COL6A5CSTAP01040884
COL6A5MS4A2Q01362767
COL6A5CMA1P23946650
COL6A5COL6A2P12110564
COL6A5COL5A2P05997485
COL6A5COL5A1P20908484
COL6A5COL6A1P12109482
COL6A5ARMH1Q6PIY5470
COL6A5ACAD10Q6JQN1469
COL6A5COL1A2P02464466
COL6A5ADAMTS2O95450440
COL6A5COL8A1P27658436
COL6A5COL2A1P02458416
COL6A5F2RL2O00254402
COL6A5CLCA2Q9UQC9396

IntAct

0 interactions, top by confidence:

BioGRID (6): COL6A5 (Affinity Capture-MS), COL6A5 (Affinity Capture-MS), COL6A5 (Reconstituted Complex), COL6A5 (Affinity Capture-Western), USP3 (Affinity Capture-Western), YWHAE (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2AX52, A6H584, A6NMZ7, A6X935, A8TX70, E1BMV3, E7FF10, O00339, O02668, O08746, O55123, O89029, P05099, P06681, P12111, P15989, P19823, P19827, P21180, P21941, P51942, P79263, P97278, P97279, Q0IIH7, Q0V8T0, Q0V8T5, Q0V8T6, Q0V8T7, Q0VCM5, Q14624, Q21540, Q29052, Q3SYW2, Q3T052, Q5GFL6, Q61702, Q61703, Q6DCQ6, Q70UZ7

Diamond homologs: A2AX52, A6H584, A6NMZ7, A6QLN9, A8TX70, E7FF10, O00339, O08746, O42401, O75578, O89029, P05099, P05555, P11215, P12111, P15989, P20701, P20702, P34576, P51942, P61625, Q02388, Q13349, Q21281, Q21540, Q28902, Q3V0T4, Q63870, Q642A6, Q6PCB0, Q6UXI7, Q8C6K9, Q8NFW1, Q8R2Z5, Q90615, Q91145, Q923P0, Q95LI2, Q96P44, Q9P218

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

406 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance321
Likely benign55
Benign12

Top pathogenic / likely-pathogenic (0)

SpliceAI

6467 predictions. Top by Δscore:

VariantEffectΔscore
3:130345977:GCTGG:Gdonor_gain1.0000
3:130345979:TGGG:Tdonor_loss1.0000
3:130345980:GG:Gdonor_gain1.0000
3:130345981:GG:Gdonor_gain1.0000
3:130345982:GTAA:Gdonor_loss1.0000
3:130345983:T:Adonor_loss1.0000
3:130376223:T:Gacceptor_gain1.0000
3:130376227:A:AGacceptor_gain1.0000
3:130376227:ATTTT:Aacceptor_gain1.0000
3:130376228:T:Gacceptor_gain1.0000
3:130376231:T:Aacceptor_gain1.0000
3:130376235:A:AGacceptor_gain1.0000
3:130376235:AG:Aacceptor_gain1.0000
3:130376235:AGG:Aacceptor_gain1.0000
3:130376236:G:GAacceptor_gain1.0000
3:130376236:GG:Gacceptor_gain1.0000
3:130376236:GGG:Gacceptor_gain1.0000
3:130376236:GGGC:Gacceptor_gain1.0000
3:130376236:GGGCC:Gacceptor_gain1.0000
3:130391613:G:GGdonor_gain1.0000
3:130394886:GCA:Gacceptor_loss1.0000
3:130394887:CA:Cacceptor_loss1.0000
3:130394888:A:AGacceptor_gain1.0000
3:130394888:AGTCT:Aacceptor_gain1.0000
3:130394889:G:GAacceptor_gain1.0000
3:130394889:GT:Gacceptor_gain1.0000
3:130394889:GTC:Gacceptor_gain1.0000
3:130394889:GTCT:Gacceptor_gain1.0000
3:130394889:GTCTG:Gacceptor_gain1.0000
3:130395462:ACCA:Adonor_gain1.0000

AlphaMissense

17346 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:130376267:T:CF33S0.986
3:130376413:T:CF82L0.986
3:130376415:C:AF82L0.986
3:130376415:C:GF82L0.986
3:130388732:T:CF672L0.985
3:130388734:C:AF672L0.985
3:130388734:C:GF672L0.985
3:130376270:T:CL34P0.984
3:130469013:G:CA2337P0.984
3:130376278:A:CS37R0.983
3:130376280:C:AS37R0.983
3:130376280:C:GS37R0.983
3:130376377:G:CA70P0.983
3:130376588:T:AV140D0.983
3:130376510:T:CL114P0.982
3:130379577:T:CL276P0.981
3:130440225:G:CD1963H0.981
3:130440723:A:CS2129R0.981
3:130440725:C:AS2129R0.981
3:130440725:C:GS2129R0.981
3:130376381:T:CL71P0.980
3:130388913:T:CL732P0.980
3:130376275:G:CD36H0.978
3:130376383:G:CA72P0.978
3:130440654:T:AC2106S0.978
3:130440655:G:CC2106S0.978
3:130379466:T:CF239S0.977
3:130388621:A:CS635R0.977
3:130388623:T:AS635R0.977
3:130388623:T:GS635R0.977

dbSNP variants (sampled 300 via entrez): RS1000011069 (3:130477402 C>G,T), RS1000030150 (3:130459395 G>A), RS1000055271 (3:130392593 T>G), RS1000058199 (3:130452890 A>G), RS1000060714 (3:130381657 C>T), RS1000077444 (3:130388285 C>T), RS1000099240 (3:130344243 A>G), RS1000110166 (3:130472241 C>T), RS1000138548 (3:130430107 G>A), RS1000159622 (3:130374910 AG>A), RS1000160525 (3:130418137 T>C), RS1000232022 (3:130478778 G>C,T), RS1000256703 (3:130394314 T>C), RS1000292961 (3:130423452 G>C), RS1000358008 (3:130361110 C>A)

Disease associations

OMIM: gene MIM:611916 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

StudyTraitp-value
GCST002301_3Body mass index1.000000e-08
GCST004748_85Lung cancer8.000000e-06
GCST008158_145Body mass index7.000000e-06
GCST010477_4Hypertension4.000000e-07
GCST010478_1Chronic kidney disease5.000000e-09
GCST012490_588Femur bone mineral density x serum urate levels interaction8.000000e-11
GCST90020028_1720Hip circumference adjusted for BMI3.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0004531urate measurement
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2364188 (PROTEIN COMPLEX GROUP)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

ChemicalActions (top 5)PubMed papers
Nickelincreases expression2
bisphenol Aincreases methylation1
sodium arseniteincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
bisphenol Saffects cotreatment, increases methylation1
MT19c compounddecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophendecreases expression1
Benzo(a)pyreneaffects methylation1
Lipopolysaccharidesaffects response to substance, increases expression1
Triclosanincreases expression1
Aflatoxin B1increases methylation1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.