COL6A2

gene
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Summary

COL6A2 (collagen type VI alpha 2 chain, HGNC:2212) is a protein-coding gene on chromosome 21q22.3, encoding Collagen alpha-2(VI) chain (P12110). Collagen VI acts as a cell-binding protein.

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.

Source: NCBI Gene 1292 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): collagen 6-related myopathy (Definitive, ClinGen) — +6 more curated relationships
  • GWAS associations: 10
  • Clinical variants (ClinVar): 2,385 total — 158 pathogenic, 89 likely-pathogenic
  • Phenotypes (HPO): 96
  • Druggable target: yes
  • MANE Select transcript: NM_001849

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2212
Approved symbolCOL6A2
Namecollagen type VI alpha 2 chain
Location21q22.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000142173
Ensembl biotypeprotein_coding
OMIM120240
Entrez1292

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 34 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000300527, ENST00000397763, ENST00000409416, ENST00000413758, ENST00000436769, ENST00000460886, ENST00000485591, ENST00000857090, ENST00000857091, ENST00000857092, ENST00000857093, ENST00000857094, ENST00000857095, ENST00000857096, ENST00000857097, ENST00000857098, ENST00000857099, ENST00000857100, ENST00000857101, ENST00000857102, ENST00000857103, ENST00000857104, ENST00000857105, ENST00000857106, ENST00000857107, ENST00000857108, ENST00000857109, ENST00000934971, ENST00000934972, ENST00000968878, ENST00000968879, ENST00000968880, ENST00000968881, ENST00000968882, ENST00000968883, ENST00000968884

RefSeq mRNA: 3 — MANE Select: NM_001849 NM_001849, NM_058174, NM_058175

CCDS: CCDS13728, CCDS13729, CCDS13730

Canonical transcript exons

ENST00000300527 — 28 exons

ExonStartEnd
ENSE000009526654611145046111591
ENSE000009526674611280446112824
ENSE000009526744611740046117453
ENSE000009526784611978846119850
ENSE000009526834612249646122531
ENSE000009526914613195446132848
ENSE000009526954611903046119119
ENSE000009526964612051546120577
ENSE000009526974612287546122937
ENSE000009526994612106146121123
ENSE000009527044611787446117936
ENSE000009527054612488546124920
ENSE000009527074611861446118676
ENSE000011103984612650346126541
ENSE000011338594612578546126237
ENSE000011340484611197946112577
ENSE000012188804612526646125311
ENSE000012192634612465146124713
ENSE000012192674612210846122158
ENSE000012193024612546546125617
ENSE000012194514611400846114073
ENSE000013323694612155646121618
ENSE000034730004611600946116053
ENSE000034773094611587246115925
ENSE000035645624611665146116677
ENSE000035893684611637746116403
ENSE000036522734611677046116814
ENSE000039950854609811246098173

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 99.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 451.5416 / max 5360.4768, expressed in 1512 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
189651438.58131509
1896524.8565616
1896531.7477476
1896661.6808549
1896551.6699562
1896501.2871540
1896650.7219390
1896780.5469307
1896840.2258123
1896830.2237142

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225599.84gold quality
right coronary arteryUBERON:000162599.80gold quality
descending thoracic aortaUBERON:000234599.76gold quality
ascending aortaUBERON:000149699.74gold quality
thoracic aortaUBERON:000151599.74gold quality
body of uterusUBERON:000985399.74gold quality
lower esophagus muscularis layerUBERON:003583399.73gold quality
lower esophagusUBERON:001347399.72gold quality
esophagogastric junction muscularis propriaUBERON:003584199.72gold quality
muscle layer of sigmoid colonUBERON:003580599.71gold quality
mucosa of stomachUBERON:000119999.70gold quality
left uterine tubeUBERON:000130399.70gold quality
aortaUBERON:000094799.69gold quality
endocervixUBERON:000045899.68gold quality
coronary arteryUBERON:000162199.68gold quality
saphenous veinUBERON:000731899.68gold quality
left coronary arteryUBERON:000162699.67gold quality
popliteal arteryUBERON:000225099.66gold quality
tibial arteryUBERON:000761099.66gold quality
cartilage tissueUBERON:000241899.65gold quality
right ovaryUBERON:000211899.64gold quality
left ovaryUBERON:000211999.59gold quality
myometriumUBERON:000129699.51gold quality
omental fat padUBERON:001041499.45gold quality
gall bladderUBERON:000211099.40gold quality
peritoneumUBERON:000235899.40gold quality
deciduaUBERON:000245099.40gold quality
colonic epitheliumUBERON:000039799.38gold quality
adipose tissue of abdominal regionUBERON:000780899.38gold quality
urethraUBERON:000005799.37gold quality

Single-cell (SCXA)

Detected in 46 experiment(s), a significant marker in 43.

ExperimentMarker?Max mean expression
E-HCAD-24yes4320.46
E-MTAB-6701yes3602.60
E-MTAB-8142yes3506.70
E-MTAB-8322yes2972.40
E-MTAB-8410yes2544.00
E-ANND-2yes2264.62
E-HCAD-11yes2254.07
E-MTAB-9906yes2215.92
E-MTAB-9841yes1859.06
E-CURD-88yes1569.68
E-CURD-122yes1561.11
E-MTAB-5061yes1504.94
E-MTAB-10485yes1215.88
E-MTAB-7407yes1186.00
E-CURD-46yes1039.97

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SMAD3, SMAD7

miRNA regulators (miRDB)

7 targeting COL6A2, 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-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-568299.8972.561005
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-6722-3P99.4567.621919

Literature-anchored findings (GeneRIF, showing 30)

  • Haplotype analysis clearly suggested linkage of Ullrich muscular dystrophy to the COL6A1/2 locus in two cases and to the COL6A3 loci in the third case. In the remaining nine patients, primary collagen VI involvement was excluded (PMID:12011280)
  • the C-terminal globular domain of COL6A2 is not essential for triple-helix formation but is critical for microfibrillar assembly in Ullrich congenital muscular dystrophy (PMID:12218063)
  • A case of Ullrich disease is associated with complete deficiency of collagen VI and compound heterozygous mutations in the collagen VI alpha 2 gene with absence of microfibrils on electron microscopy. (PMID:12297580)
  • Bethlem myopathy is an autosomal dominantly inherited myopathy with contractures, caused by mutations in COL6A1 gene, COL6A2 gene or COL6A3 gene. (PMID:12374585)
  • In Ullrich syndrome, a heterozygous G-to-A substitution at position +5 in intron 23 & the corresponding heterozygous 6-bp deletion in exon 26 which deleted 1 of the 2 tandem repeats of the sequence CATCGG in nt 2268-2273 & 2274-2279 in COL6A2 ORF. (PMID:14981181)
  • dominant mutations are common in Ullrich congenital muscular dystrophy (UCMD). (PMID:15563506)
  • diminished COL6A2 mRNA expression found to be primary pathogenic mechanism in UCMD patient (PMID:16075202)
  • This study demonstrates a homogenoeous overexpression of the genes encoding for alpha1 and alpha2 chains of collagen type VI in nuchal skin of human trisomy 21 fetuses. (PMID:17602442)
  • Study reports 10 unrelated patients with a Ullrich congenital muscular dystrophy clinical phenotype and de novo dominant negative heterozygous splice mutations in COL6A1, COL6A2 and COL6A3. (PMID:18366090)
  • Results describe the characteristic features of myosclerosis myopathy with a homozygous collagen type 6A2 mutation responsible for a peculiar pattern of collagen VI defects. (PMID:18852439)
  • Four patients affected by Ullrich congenital muscular dystrophy and carrying unusual mutations of COL6 genes affecting RNA splicing, were identified. (PMID:19309692)
  • The alpha2(VI) chain modulates matrix-metalloproteinase (MMP) availability by sequestering proMMPs in the extracellular matrix, blocking proteolytic activity. (PMID:19698785)
  • the C2A splice variant has a role in recessive COL6A2 C-globular missense mutations in Ullrich congenital muscular dystrophy (PMID:20106987)
  • A deletion within intron 1A of the COL6A2 gene, occurring in compound heterozygosity with a small deletion in exon 28, was identified in a BM patient. (PMID:20302629)
  • Homozygous COL6A2 mutation, p.Asp215Asn, was identified in both affected siblings. We conclude that the COL6A2 p.Asp215Asn mutation is likely to be responsible for PME (Progressive Myoclonus Epilepsy) in this family. (PMID:23138527)
  • COL6A2 is overexpressed in Down syndrome-affected umbilical cords at early and term gestational ages. (PMID:23452080)
  • Mutations in each of the three collagen VI genes, COL6A1, COL6A2 and COL6A3, cause four types of muscle disorders: Ullrich congenital muscular dystrophy, Bethlem myopathy, limb-girdle muscular dystrophy, and autosomal recessive myosclerosis. (Review) (PMID:24443028)
  • In UCMD, 8 mutations were identified in COL6A2 in Chinese patients. (PMID:24801232)
  • 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. (PMID:25204870)
  • Mutations in COL6A2 gene are associated with aberrant mitochondria in Bethlem myopathy. (PMID:25533456)
  • binding of collagen VI to NG2 is essential for the direction of tendon fibroblasts migration in vitro. (PMID:26944560)
  • 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. (PMID:27563703)
  • Tendon Extracellular Matrix Remodeling and Defective Cell Polarization in the Presence of Collagen VI Mutations. (PMID:32053901)
  • 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. (PMID:32350230)
  • Use of RNAsequencing to detect abnormal transcription of the collagen alpha2 (VI) chain gene that can lead to Bethlem myopathy. (PMID:33537799)
  • Collagen type VIalpha1 and 2 repress the proliferation, migration and invasion of bladder cancer cells. (PMID:33982770)
  • The Presentation of Two Unrelated Clinical Cases from the Republic of North Ossetia-Alania with the Same Previously Undescribed Variant in the COL6A2 Gene. (PMID:36292982)
  • Role of COL6A2 in malignant progression and temozolomide resistance of glioma. (PMID:36521657)
  • Extracellular Matrix Disorganization and Sarcolemmal Alterations in COL6-Related Myopathy Patients with New Variants of COL6 Genes. (PMID:36982625)
  • A novel interplay between PRC2 and miR-3189 regulates epithelial-mesenchymal transition (EMT) via modulating COL6A2 in glioblastoma. (PMID:38860406)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocol6a2ENSDARG00000061436
mus_musculusCol6a2ENSMUSG00000020241
rattus_norvegicusCol6a2ENSRNOG00000001254

Paralogs (37): COL9A2 (ENSG00000049089), COL23A1 (ENSG00000050767), COL11A1 (ENSG00000060718), COL17A1 (ENSG00000065618), COL5A3 (ENSG00000080573), COL4A4 (ENSG00000081052), COL16A1 (ENSG00000084636), COL9A3 (ENSG00000092758), COL20A1 (ENSG00000101203), COL1A1 (ENSG00000108821), COL9A1 (ENSG00000112280), COL7A1 (ENSG00000114270), COL21A1 (ENSG00000124749), COL5A1 (ENSG00000130635), COL4A2 (ENSG00000134871), COL2A1 (ENSG00000139219), COL6A1 (ENSG00000142156), EDA (ENSG00000158813), COL26A1 (ENSG00000160963), COL1A2 (ENSG00000164692), COL3A1 (ENSG00000168542), COL4A3 (ENSG00000169031), COL22A1 (ENSG00000169436), COL24A1 (ENSG00000171502), COL18A1 (ENSG00000182871), EMID1 (ENSG00000186998), COL4A1 (ENSG00000187498), COL4A5 (ENSG00000188153), COL25A1 (ENSG00000188517), COL27A1 (ENSG00000196739), COL13A1 (ENSG00000197467), COL4A6 (ENSG00000197565), COL11A2 (ENSG00000204248), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

Collagen alpha-2(VI) chainP12110 (reviewed: P12110)

All UniProt accessions (4): P12110, A0A384MDP3, C9JH44, H7C0M5

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). Interacts with CSPG4.

Subcellular location. Secreted. Extracellular space. Extracellular matrix. Membrane.

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. Bethlem myopathy 1B (BTHLM1B) [MIM:620725] A form of Bethlem myopathy, a slowly progressive muscular dystrophy characterized by joint contractures, most frequently affecting the elbows and ankles, and muscle weakness and wasting involving the proximal and extensor muscles more than the distal and flexor ones. The clinical onset more often occurs in childhood or adulthood, but it can be prenatal with decreased fetal movements or neonatal with hypotonia. The hallmark of Bethlem myopathy is long finger flexion contractures. Inheritance can be autosomal dominant or autosomal recessive. The disease is caused by variants affecting the gene represented in this entry. Ullrich congenital muscular dystrophy 1B (UCMD1B) [MIM:620727] A form of Ullrich congenital muscular dystrophy, a disease characterized by generalized muscle weakness and striking hypermobility of distal joints in conjunction with variable contractures of more proximal joints and normal intelligence. Additional findings may include kyphoscoliosis, protruded calcanei, and follicular hyperkeratosis (rough skin). More severely affected patients manifest at birth and never achieve independent ambulation, while patients with milder phenotypes might maintain ambulation into adulthood. Inheritance can be autosomal dominant or autosomal recessive. The disease is caused by variants affecting the gene represented in this entry. Myosclerosis autosomal recessive (MYOSAR) [MIM:255600] A condition characterized by chronic inflammation of skeletal muscle with hyperplasia of the interstitial connective tissue. The clinical picture includes slender muscles with firm ‘woody’ consistency and restriction of movement of many joints because of muscle contractures. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the type VI collagen family.

Isoforms (3)

UniProt IDNamesCanonical?
P12110-12C2yes
P12110-22C2A
P12110-32C2A’

RefSeq proteins (3): NP_001840, NP_478054, NP_478055 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002035VWF_ADomain
IPR008160CollagenRepeat
IPR036465vWFA_dom_sfHomologous_superfamily
IPR052229Collagen-VI/PIFFamily

Pfam: PF00092, PF01391

UniProt features (63 total): sequence variant 29, compositionally biased region 6, glycosylation site 6, short sequence motif 5, splice variant 4, region of interest 4, domain 3, modified residue 2, sequence conflict 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9GTUELECTRON MICROSCOPY3.14

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P12110-F169.580.18

Functional residue map

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

Post-translational modifications (2): 701, 705

Glycosylation sites (6): 140, 327, 630, 785, 897, 954

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: 428 (showing top): PAL_PRMT5_TARGETS_UP, GOCC_COLLAGEN_TRIMER, REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH, HUMMERICH_SKIN_CANCER_PROGRESSION_DN, CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN, MODULE_66, BROWNE_HCMV_INFECTION_48HR_DN, MARTINEZ_RB1_TARGETS_UP, ROZANOV_MMP14_TARGETS_UP, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, GNF2_CDH11, GOBP_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, RIGGI_EWING_SARCOMA_PROGENITOR_DN

GO Biological Process (5): cell adhesion (GO:0007155), response to UV (GO:0009411), response to glucose (GO:0009749), phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0043491), neuron apoptotic process (GO:0051402)

GO Molecular Function (3): collagen binding (GO:0005518), extracellular matrix structural constituent conferring tensile strength (GO:0030020), protein binding (GO:0005515)

GO Cellular Component (11): extracellular region (GO:0005576), collagen type VI trimer (GO:0005589), obsolete extracellular space (GO:0005615), endoplasmic reticulum lumen (GO:0005788), extracellular matrix (GO:0031012), protein-containing complex (GO:0032991), sarcolemma (GO:0042383), extracellular exosome (GO:0070062), extracellular vesicle (GO:1903561), collagen trimer (GO:0005581), membrane (GO:0016020)

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 anatomical structure2
cellular process1
response to light stimulus1
response to hexose1
intracellular signaling cassette1
apoptotic process1
protein-containing complex binding1
extracellular matrix structural constituent1
binding1
collagen beaded filament1
von-Willerbrand-factor-A-domain-rich collagen trimer1
extracellular protein-containing complex1
endoplasmic reticulum1
intracellular organelle lumen1
external encapsulating structure1
cellular_component1
plasma membrane1
extracellular vesicle1
extracellular region1
vesicle1
extracellular membrane-bounded organelle1
protein-containing complex1

Protein interactions and networks

STRING

2538 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COL6A2COL6A3P12111978
COL6A2COL6A1P12109965
COL6A2LAMB1P07942818
COL6A2A0A087WVV2A0A087WVV2784
COL6A2FN1P02751758
COL6A2COL1A1P02452716
COL6A2BGNP13247701
COL6A2PFKLP17858674
COL6A2NID1P14543639
COL6A2ICAM1P05362634
COL6A2ITGA5P08648632
COL6A2LAMC1P11047631
COL6A2TNXBP22105623
COL6A2LAMA5O15230619
COL6A2DMDP11532618

IntAct

139 interactions, top by confidence:

ABTypeScore
C1QTNF9C1QTNF9Bpsi-mi:“MI:0914”(association)0.780
CA10WDHD1psi-mi:“MI:0914”(association)0.640
MMP9TIMP1psi-mi:“MI:0914”(association)0.640
DKKL1DENND11psi-mi:“MI:0914”(association)0.640
MMP2COL4A1psi-mi:“MI:0914”(association)0.640
PLA2G10CHEK1psi-mi:“MI:0914”(association)0.530
TAFA4NRP1psi-mi:“MI:0914”(association)0.530
WNT10BLRP6psi-mi:“MI:0914”(association)0.530
SCGB1D4EGFRpsi-mi:“MI:0914”(association)0.530
COLGALT2COL1A1psi-mi:“MI:0914”(association)0.530
DEFB121COL6A2psi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
INSL5COCHpsi-mi:“MI:0914”(association)0.530
C1QTNF9BPLOD3psi-mi:“MI:0914”(association)0.530
PLOD3COL4A1psi-mi:“MI:0914”(association)0.530
CTSGMANBApsi-mi:“MI:0914”(association)0.530
PLOD3PLOD2psi-mi:“MI:0914”(association)0.530
GPIHBP1ADAM10psi-mi:“MI:0914”(association)0.530
LAIR2LAMA5psi-mi:“MI:0914”(association)0.530
EDN3MGRN1psi-mi:“MI:0914”(association)0.530

BioGRID (109): COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS)

ESM2 similar proteins: A2AX52, A6H584, A6NMZ7, A8K7I4, A8TX70, E1BMV3, O35701, O42401, O54890, P05099, P12110, P12111, P13612, P13944, P15988, P15989, P17301, P18563, P18564, P20785, P21941, P51942, P53710, P56652, P61622, P97280, Q00651, Q02788, Q04857, Q06033, Q1RPR6, Q2TU62, Q5RB37, Q60847, Q61704, Q62469, Q62935, Q63416, Q6AYF4, Q6PT52

Diamond homologs: A2AX52, A6H584, A6NMZ7, A6QLN9, A8TX70, E7FF10, O00339, O08746, O15232, O35701, O42401, O43405, O75578, O89029, O95460, P05555, P12109, P12110, P12111, P13944, P15989, P17301, P18614, P20702, P20785, P32018, P34576, P53710, P56199, P61622, P61625, P84552, Q02388, Q04857, Q05707, Q21281, Q21540, Q28295, Q28902, Q2UY09

SIGNOR signaling

1 interactions.

AEffectBMechanism
COL6A2up-regulatesECM_synthesis

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 160 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Negative regulation of TCF-dependent signaling by WNT ligand antagonists531.9×4e-05
WNT ligand biogenesis and trafficking518.9×4e-04
Collagen biosynthesis and modifying enzymes1218.3×7e-10
Collagen chain trimerization716.2×3e-05
Collagen degradation1015.7×1e-07
Beta defensins614.6×2e-04
Defensins612.8×4e-04
Assembly of collagen fibrils and other multimeric structures712.5×1e-04

GO biological processes:

GO termPartnersFoldFDR
collagen biosynthetic process537.4×7e-05
cell fate commitment714.7×1e-04
collagen fibril organization914.3×2e-05
canonical Wnt signaling pathway1010.9×2e-05
defense response to Gram-negative bacterium78.4×3e-03
transforming growth factor beta receptor signaling pathway77.9×3e-03
neuron differentiation96.4×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

2385 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic158
Likely pathogenic89
Uncertain significance829
Likely benign660
Benign141

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1029383NM_058174.3(COL6A2):c.2554C>T (p.Gln852Ter)Pathogenic
1060752NM_001849.4(COL6A2):c.2097_2098delinsTA (p.Gly700Ser)Pathogenic
1061166NM_001849.4(COL6A2):c.2832_2927del (p.Phe944_Ala975del)Pathogenic
1068296NM_001849.4(COL6A2):c.1053+2T>GPathogenic
1070014NC_000021.8:g.(?_47529674)_47540994delPathogenic
1070015NC_000021.8:g.(?_47533070)_47584395delPathogenic
1070123NM_001849.4(COL6A2):c.2023C>T (p.Gln675Ter)Pathogenic
1070535NM_001849.4(COL6A2):c.999+9_1053+32delinsGCTGAAGGAGGGGTGCAAACGGCCCTTACCCGGTTTCCAGGGTCTCCCTTGCAGCCTTCAPathogenic
1071804NM_001849.4(COL6A2):c.955-1G>CPathogenic
1072953NM_001849.4(COL6A2):c.1053+2T>APathogenic
1073260NM_001849.4(COL6A2):c.998del (p.Lys333fs)Pathogenic
1073867NM_001849.4(COL6A2):c.954G>C (p.Lys318Asn)Pathogenic
1073909NM_001849.4(COL6A2):c.2560_2569dup (p.Glu857fs)Pathogenic
1074374NM_001849.4(COL6A2):c.1075dup (p.Glu359fs)Pathogenic
1075831NM_001849.4(COL6A2):c.2500_2501del (p.Ile834fs)Pathogenic
1184919NM_001849.4(COL6A2):c.439C>T (p.Gln147Ter)Pathogenic
1322143NM_001849.4(COL6A2):c.869_899del (p.Ile290fs)Pathogenic
1322144NM_001849.4(COL6A2):c.2082_2083dup (p.Glu695fs)Pathogenic
1322145NM_001849.4(COL6A2):c.1479dup (p.Asp494Ter)Pathogenic
1348005NM_001849.4(COL6A2):c.821G>A (p.Gly274Asp)Pathogenic
1351958NM_001849.4(COL6A2):c.874G>A (p.Gly292Ser)Pathogenic
1358090NM_001849.4(COL6A2):c.2341C>T (p.Gln781Ter)Pathogenic
1407076NM_001849.4(COL6A2):c.1332+2T>CPathogenic
1426820NM_001849.4(COL6A2):c.2851_2852del (p.Val951fs)Pathogenic
1445193NM_001849.4(COL6A2):c.884G>A (p.Gly295Glu)Pathogenic
1451727NM_001849.4(COL6A2):c.2586dup (p.Leu863fs)Pathogenic
1452401NM_001849.4(COL6A2):c.288C>A (p.Tyr96Ter)Pathogenic
1454472NM_001849.4(COL6A2):c.2133C>A (p.Tyr711Ter)Pathogenic
1455508NC_000021.8:g.(?47536737)(47537399_?)delPathogenic
1455757NM_001849.4(COL6A2):c.884G>T (p.Gly295Val)Pathogenic

SpliceAI

3932 predictions. Top by Δscore:

VariantEffectΔscore
21:46098171:CAGG:Cdonor_loss1.0000
21:46098174:G:Cdonor_loss1.0000
21:46112937:G:GTdonor_gain1.0000
21:46114006:A:AGacceptor_gain1.0000
21:46114007:G:GGacceptor_gain1.0000
21:46115867:TTTA:Tacceptor_loss1.0000
21:46115870:A:AGacceptor_gain1.0000
21:46115870:A:Tacceptor_loss1.0000
21:46115870:AG:Aacceptor_gain1.0000
21:46115871:G:Aacceptor_gain1.0000
21:46115871:G:GGacceptor_gain1.0000
21:46115871:GGGT:Gacceptor_gain1.0000
21:46115921:GACAG:Gdonor_gain1.0000
21:46115926:G:GGdonor_gain1.0000
21:46115926:GT:Gdonor_loss1.0000
21:46115927:T:Adonor_loss1.0000
21:46116003:TCACA:Tacceptor_loss1.0000
21:46116004:CACA:Cacceptor_loss1.0000
21:46116005:A:AGacceptor_gain1.0000
21:46116005:ACAG:Aacceptor_gain1.0000
21:46116006:CAG:Cacceptor_loss1.0000
21:46116007:A:AGacceptor_gain1.0000
21:46116007:AG:Aacceptor_gain1.0000
21:46116007:AGG:Aacceptor_gain1.0000
21:46116008:G:GAacceptor_gain1.0000
21:46116008:GG:Gacceptor_gain1.0000
21:46116008:GGG:Gacceptor_gain1.0000
21:46116008:GGGA:Gacceptor_gain1.0000
21:46116052:AGGTG:Adonor_loss1.0000
21:46116054:G:GAdonor_loss1.0000

AlphaMissense

6637 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
21:46125512:A:CS622R1.000
21:46125514:C:AS622R1.000
21:46125514:C:GS622R1.000
21:46125516:C:TS623F1.000
21:46125901:T:AW696R1.000
21:46125901:T:CW696R1.000
21:46125903:G:CW696C1.000
21:46125903:G:TW696C1.000
21:46116027:G:TG292C0.999
21:46116037:G:AG295E0.999
21:46125300:G:AC602Y0.999
21:46125509:G:CD621H0.999
21:46125510:A:CD621A0.999
21:46125510:A:TD621V0.999
21:46125513:G:TS622I0.999
21:46125515:T:CS623P0.999
21:46125516:C:AS623Y0.999
21:46125521:A:CS625R0.999
21:46125523:C:AS625R0.999
21:46125523:C:GS625R0.999
21:46125539:T:CF631L0.999
21:46125540:T:CF631S0.999
21:46125540:T:GF631C0.999
21:46125541:C:AF631L0.999
21:46125541:C:GF631L0.999
21:46125561:T:AV638D0.999
21:46125811:A:CS666R0.999
21:46125813:C:AS666R0.999
21:46125813:C:GS666R0.999
21:46125887:T:AV691D0.999

dbSNP variants (sampled 300 via entrez): RS1000088379 (21:46121235 A>C), RS1000213329 (21:46128229 C>G), RS1000252994 (21:46097995 C>T), RS1000308445 (21:46100635 G>A), RS1000381308 (21:46103865 A>G), RS1000496223 (21:46114298 G>A), RS1000595507 (21:46118656 A>T), RS1000645836 (21:46125723 A>C,G), RS1000659579 (21:46110078 T>G), RS1000671092 (21:46099302 A>G), RS1000813287 (21:46105538 A>G), RS1000821297 (21:46130493 A>ACAGGG), RS1000846239 (21:46105268 C>T), RS1000917621 (21:46111078 T>C,G), RS1000968931 (21:46115385 A>G)

Disease associations

OMIM: gene MIM:120240 | disease phenotypes: MIM:158810, MIM:255600, MIM:620725, MIM:620727, MIM:254090, MIM:117000, MIM:118220

GenCC curated gene-disease

DiseaseClassificationInheritance
Ullrich congenital muscular dystrophy 1BDefinitiveAutosomal dominant
Bethlem myopathy 1AStrongAutosomal dominant
Ullrich congenital muscular dystrophy 1AStrongAutosomal dominant
myosclerosisSupportiveAutosomal recessive
Bethlem myopathySupportiveAutosomal dominant
Ullrich congenital muscular dystrophySupportiveAutosomal dominant

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
collagen 6-related myopathyDefinitiveAD
collagen 6-related myopathyDefinitiveAR

Mondo (14): Bethlem myopathy 1A (MONDO:0024530), myosclerosis (MONDO:0009714), Bethlem myopathy 1B (MONDO:0958233), Ullrich congenital muscular dystrophy 1B (MONDO:0958235), Ullrich congenital muscular dystrophy 1A (MONDO:0009681), myopathy (MONDO:0005336), collagen 6-related myopathy (MONDO:0100225), Bethlem myopathy (MONDO:0008029), congenital myopathy (MONDO:0019952), limb-girdle muscular dystrophy (MONDO:0016971), muscular dystrophy (MONDO:0020121), congenital muscular dystrophy (MONDO:0019950), Charcot-Marie-Tooth disease (MONDO:0015626), Ullrich congenital muscular dystrophy (MONDO:0000355)

Orphanet (9): Bethlem muscular dystrophy (Orphanet:610), Myosclerosis (Orphanet:289380), Ullrich congenital muscular dystrophy (Orphanet:75840), Qualitative or quantitative defects of collagen 6 (Orphanet:207090), Congenital myopathy (Orphanet:97245), Limb-girdle muscular dystrophy (Orphanet:263), Muscular dystrophy (Orphanet:98473), Congenital muscular dystrophy (Orphanet:97242), Charcot-Marie-Tooth disease/Hereditary motor and sensory neuropathy (Orphanet:166)

HPO phenotypes

96 total (30 of 96 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000174Abnormal palate morphology
HP:0000218High palate
HP:0000347Micrognathia
HP:0000467Neck muscle weakness
HP:0000470Short neck
HP:0000473Torticollis
HP:0000565Esotropia
HP:0000962Hyperkeratosis
HP:0001073Cigarette-paper scars
HP:0001181Adducted thumb
HP:0001220Interphalangeal joint contracture of finger
HP:0001238Slender finger
HP:0001239Wrist flexion contracture
HP:0001249Intellectual disability
HP:0001252Hypotonia
HP:0001270Motor delay
HP:0001288Gait disturbance
HP:0001290Generalized hypotonia
HP:0001324Muscle weakness
HP:0001371Flexion contracture
HP:0001382Joint hypermobility
HP:0001558Decreased fetal movement
HP:0001771Achilles tendon contracture
HP:0002086Abnormality of the respiratory system
HP:0002359Frequent falls
HP:0002460Distal muscle weakness
HP:0002515Waddling gait
HP:0002650Scoliosis

GWAS associations

10 associations (top):

StudyTraitp-value
GCST005170_24Intraocular pressure8.000000e-09
GCST005667_43Central corneal thickness2.000000e-09
GCST008839_203Height2.000000e-09
GCST010002_78Refractive error2.000000e-36
GCST90000025_701Appendicular lean mass3.000000e-22
GCST90000654_72Central corneal thickness2.000000e-08
GCST90020025_1778Waist-to-hip ratio adjusted for BMI4.000000e-09
GCST90020027_397Waist-hip index2.000000e-09
GCST90020029_167Waist circumference adjusted for body mass index2.000000e-08
GCST90020029_168Waist circumference adjusted for body mass index1.000000e-08

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004695intraocular pressure measurement
EFO:0005213central corneal thickness
EFO:0004980appendicular lean mass
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0007789BMI-adjusted waist circumference

MeSH disease descriptors (6)

DescriptorNameTree numbers
D002607Charcot-Marie-Tooth DiseaseC10.500.300.200; C10.574.500.495.200; C10.668.829.800.300.200; C16.131.666.300.200; C16.320.400.375.200
D009136Muscular DystrophiesC05.651.534.500; C10.668.491.175.500; C16.320.577
D049288Muscular Dystrophies, Limb-GirdleC05.651.534.500.280; C10.668.491.175.500.149; C16.320.577.280
C535436Bethlem myopathy (supp.)
C564968Myosclerosis, Autosomal Recessive (supp.)
C537521Scleroatonic muscular dystrophy (supp.)

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

63 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, increases methylation, affects cotreatment4
sodium arseniteaffects methylation, affects cotreatment, increases expression3
Cadmium Chlorideaffects cotreatment, decreases expression, increases abundance, increases expression3
Benzo(a)pyreneaffects methylation, decreases methylation, increases methylation2
Estradiolaffects cotreatment, decreases expression, increases expression2
bisphenol Fincreases expression1
peracetylated N-azidoacetylmannosaminedecreases expression1
testosterone enanthateaffects expression1
propionaldehydeincreases expression1
bisphenol Adecreases expression1
deoxynivalenoldecreases expression1
lead acetateaffects cotreatment, increases expression1
tris(2-butoxyethyl) phosphateaffects expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
chromous chlorideaffects cotreatment, increases expression1
chromic oxideaffects cotreatment, increases expression1
aflatoxin B2increases methylation1
CGP 52608affects binding, increases reaction1
enniatinsdecreases expression1
monomethylarsonous aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
clothianidinincreases expression1
bisphenol Bincreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
licochalcone Bincreases expression1
jinfukangincreases expression1
(+)-JQ1 compounddecreases expression1
bisphenol AFincreases expression1

Cellosaurus cell lines

11 cell lines: 5 finite cell line, 5 transformed cell line, 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_4T46GM23308Finite cell lineFemale
CVCL_4T49GM23681Transformed cell lineMale
CVCL_4T52GM23778Finite cell lineMale
CVCL_4T53GM23782Transformed cell lineMale
CVCL_4T59GM24224Finite cell lineMale
CVCL_4T60GM24231Transformed cell lineMale
CVCL_4T61GM24232Transformed cell lineFemale
CVCL_A9ZIGM27913Finite cell lineFemale
CVCL_B0IEGM28234Finite cell lineFemale
CVCL_B2UUAbcam HEK293T COL6A2 KOTransformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00120055PHASE4COMPLETEDAssociation Between Systemic Exposure of Atorvastatin and Metabolites and Atorvastatin-induced Myotoxicity
NCT03633565PHASE4UNKNOWNComparative Study of Strategies for Management of Duchenne Myopathy (DM)
NCT01882400PHASE4COMPLETEDAssessment of Response to Treatment of Osteoporosis With Oral Bisphosphonates in Patients With Muscular Dystrophy
NCT01422200PHASE4COMPLETEDFlu Vaccine Study in Neuromuscular Patients 2011
NCT01225614PHASE3UNKNOWNEfficacy and Tolerance of Early Launching of Nocturnal Non Invasive
NCT03783923PHASE3TERMINATEDA Study of Deflazacort (Emflaza®) in Participants With Limb-Girdle Muscular Dystrophy 2I (LGMD2I)
NCT06246513PHASE3ACTIVE_NOT_RECRUITINGA Trial to Learn More About an Experimental Gene Therapy Called Bidridistrogene Xeboparvovec (SRP-9003) as a Possible Treatment for Limb Girdle Muscular Dystrophy 2E/R4
NCT01254019PHASE3COMPLETEDA Clinical Study to Assess the Efficacy and Safety of GSK2402968 in Subjects With Duchenne Muscular Dystrophy
NCT01480245PHASE3TERMINATEDOpen Label Study of GSK2402968 in Subjects With Duchenne Muscular Dystrophy
NCT01803412PHASE3TERMINATEDA Study of the Safety, Tolerability & Efficacy of Long-term Administration of Drisapersen in US & Canadian Subjects
NCT01826487PHASE3COMPLETEDPhase 3 Study of Ataluren in Participants With Nonsense Mutation Duchenne Muscular Dystrophy (nmDMD)
NCT01890798PHASE3WITHDRAWNDrisapersen Duchenne Muscular Dystrophy (DMD) Treatment Protocol
NCT02090959PHASE3TERMINATEDAn Extension Study of Ataluren (PTC124) in Participants With Nonsense Mutation Dystrophinopathy
NCT02432885PHASE3COMPLETEDMyocardial Fibrosis Progression in Duchenne and Becker Muscular Dystrophy - ACE Inhibitor Therapy Trial
NCT03179631PHASE3COMPLETEDLong-Term Outcomes of Ataluren in Duchenne Muscular Dystrophy
NCT05126758PHASE3ACTIVE_NOT_RECRUITINGA Study of Deramiocel (CAP-1002) in Ambulatory and Non-Ambulatory Patients With Duchenne Muscular Dystrophy
NCT07587242PHASE3NOT_YET_RECRUITINGA Phase 3 Study to Evaluate the Safety and Efficacy of AOC 1044 (Also Referred to as Delpacibart Zotadirsen) in Participants With DMD With Gene Mutations Amenable to Exon 44 Skipping
NCT07608432PHASE3RECRUITINGEfficacy, Safety, and Tolerability of Zeleciment Rostudirsen (DYNE-251) Administered Intravenously Every 4 Weeks in Ambulatory Participants With Duchenne Muscular Dystrophy (FORZETTO)
NCT04762758PHASE3UNKNOWNPhase III Trial Assessing the Efficacy and Safety of PXT3003 in CMT1A Patients
NCT01438788PHASE2COMPLETEDLow Protein Diet in Patients With Collagen VI Related Myopathies
NCT04054375PHASE2COMPLETEDWeekly Steroids in Muscular Dystrophy
NCT01153932PHASE2COMPLETEDPhase II Doubleblind Exploratory Study of GSK2402968 in Ambulant Subjects With Duchenne Muscular Dystrophy
NCT01462292PHASE2COMPLETEDA Clinical Study to Assess Two Doses of GSK2402968 in Subjects With Duchenne Muscular Dystrophy (DMD)
NCT01910649PHASE2TERMINATEDA Phase I/II, Open Label, Escalating Dose, Pilot Study to Assess Effect, Safety, Tolerability and PK of Multiple SC Doses of Drisapersen in Patients With Duchenne Muscular Dystrophy and to Assess the Potential for IV Dosing as an Alternative Route of Administration
NCT03406780PHASE2COMPLETEDA Study of CAP-1002 in Ambulatory and Non-Ambulatory Patients With Duchenne Muscular Dystrophy
NCT05479981PHASE2COMPLETEDExtension of AOC 1001-CS1 (MARINA) Study in Adult Myotonic Dystrophy Type 1 (DM1) Patients
NCT06290713PHASE2RECRUITINGVasodilator and Exercise Study for DMD (VASO-REx)
NCT06547216PHASE2ACTIVE_NOT_RECRUITINGPhase 2 Open-label Extension Study of AOC 1020 in Participants With Facioscapulohumeral Muscular Dystrophy (FSHD)
NCT07287189PHASE2RECRUITINGPhase 2 Study of SAT-3247 in Pediatric Ambulatory Patients
NCT00271635PHASE2COMPLETEDAscorbic Acid Treatment in CMT1A Trial (AATIC)
NCT01401257PHASE2COMPLETEDPhase II, Randomized, Placebo-controlled Trial in Patients With Charcot-marie-tooth Disease Type 1A
NCT02561702PHASE2COMPLETEDMexiletine for Muscle Cramps in Charcot Marie Tooth Disease
NCT02967679PHASE2COMPLETEDSERENDEM : MD1003 in Patients Suffering From Demyelinating Neuropathies, an Open Label Pilot Study
NCT03124459PHASE2TERMINATEDStudy of ACE-083 in Patients With Charcot-Marie-Tooth Disease
NCT03254199PHASE2TERMINATEDA Study to Assess the Safety and Effectiveness of FLX-787 in Subjects With Charcot-Marie-Tooth Disease Experiencing Muscle Cramps.
NCT03943290PHASE2TERMINATEDExtension Study to Evaluate the Long-Term Effects of ACE-083 in Patients With Facioscapulohumeral Muscular Dystrophy (FSHD) and Charcot-Marie Tooth (CMT) Disease Types 1 and X (CMT1 and CMTX)
NCT05777226PHASE2UNKNOWNResearch of SORD-CMT Natural History and Epalrestat Treatment
NCT06482437PHASE2COMPLETEDSafety and Efficacy of NMD670 in Adult Patients With Type 1 and Type 2 Charcot-Marie-Tooth Disease
NCT00278564PHASE1TERMINATEDStem Cell Transplantation in Idiopathic Inflammatory Myopathy Diseases
NCT00873782PHASE1COMPLETEDSafety Study of Transvenous Limb Perfusion in Human Muscular Dystrophy