COL6A3

Chr 2ADAR

collagen type VI alpha 3 chain

Also known as: BTHLM1, BTHLM1C, DYT27, UCMD1, UCMD1C

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]

Primary Disease Associations & Inheritance

Bethlem myopathy 1CMIM #620726
ADAR
Dystonia 27MIM #616411
AR
Ullrich congenital muscular dystrophy 1CMIM #620728
ADAR
652
ClinVar variants
49
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical SummaryCOL6A3
🧬
Gene-Disease Validity (ClinGen)
collagen 6-related myopathy · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

3 total gene-disease associations curated

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
49 Pathogenic / Likely Pathogenic· 400 VUS of 652 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.56LOEUF
pLI 0.000
Z-score 5.65
OE 0.45 (0.360.56)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.61Z-score
OE missense 1.04 (1.001.08)
1908 obs / 1835.0 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.45 (0.360.56)
00.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.04 (1.001.08)
00.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.10
01.21.6
LoF obs/exp: 55 / 122.5Missense obs/exp: 1908 / 1835.0Syn Z: -2.16

ClinVar Variant Classifications

652 submitted variants in ClinVar

Classification Summary

Pathogenic34
Likely Pathogenic15
VUS400
Likely Benign194
Benign3
Conflicting6
34
Pathogenic
15
Likely Pathogenic
400
VUS
194
Likely Benign
3
Benign
6
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
13
1
20
0
34
Likely Pathogenic
9
2
3
1
15
VUS
1
372
22
5
400
Likely Benign
0
20
63
111
194
Benign
0
3
0
0
3
Conflicting
6
Total23398108117652

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

COL6A3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

COL6A3-related Ullrich congenital muscular dystrophy

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

Bethlem myopathy 1C

MIM #620726

Molecular basis of disorder known

Autosomal dominantAutosomal recessive

Dystonia 27

MIM #616411

Molecular basis of disorder known

Autosomal recessive

Ullrich congenital muscular dystrophy 1C

MIM #620728

Molecular basis of disorder known

Autosomal dominantAutosomal recessive
📖
GeneReview available — COL6A3
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Collagen type VI myopathies.
Bushby KM et al.·Adv Exp Med Biol
2014Review
Top 10 resultsSearch PubMed ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →