COL11A1
protein-codingcollagen type XI alpha 1 chain, the group of Collagens
Gene summary
This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]
- COLL6
- DFNA37
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~232.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007949
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0032802
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011493
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0018601
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011493
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0016068
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0007949
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0032802
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007949
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0007949
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009226
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0019587
Submitter: ClinGen
COL11A1 was first reported in relation to autosomal dominant nonsyndromic hearing loss in 2018 (Booth et al., PMID: 30245514). Variants in COL11A1 have been reported in individuals with the following disease entities: deafness, autosomal dominant 37 (MIM:618533), fibrochondrogenesis 1 (MIM:228520), Marshall syndrome (MIM:154780), Stickler syndrome, type II (MIM:604841), and susceptibility to lumbar disc herniation (MIM:603932). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in inheritance pattern and phenotypic variability. Therefore, autosomal dominant nonsyndromic hearing loss has been split and curated as a separate disease entity. 8 variants (3 splice site, 3 frameshift, and 2 missense) that have been reported in 33 patients in 6 publications (PMIDs: 30245514, 33169910, 32427345, 33605226, 38410152, 39443691) are included in this curation. The mechanism of pathogenicity is unclear, but variants associated with autosomal dominant nonsyndromic hearing loss tend to be located within the N-terminal propeptide domain of COL11A1. This gene-disease association is supported by in situ hybridization analysis showing expression of COL11A1 in mouse temporal bones (PMID: 15141750). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This classification was approved by the ClinGen Hearing Loss GCEP on the meeting date June 18, 2025 (SOP Version 11).
Inheritance Pattern: AD
Disease ID:MONDO:0007949
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011493
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0009226
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0011493
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Ophthalmologic
Intervention: Audiologic/Otolaryngologic; Ophthalmologic
Rationale: Though the conditions may be recognizable, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; In Stickler syndrome, avoidance of risk factors related to ocular manifestations (eg, contact sports) is indicated
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COL11A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001854.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 28 | 423 | 29 | 482 | |
| missense | 10 | 58 | 1139 | 338 | 45 | 1590 |
| nonsense | 20 | 15 | 1 | 36 | ||
| start loss | 0 | |||||
| frameshift | 25 | 21 | 4 | 50 | ||
| splice donor/acceptor (+/-2bp) | 36 | 96 | 14 | 146 | ||
| Total | 91 | 192 | 1186 | 761 | 74 | 2304 |
Highest pathogenic variant AF is 0.00004363048
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001845.3 | 67 | MANE Select | |
| Ensembl | ENSP00000359114.3 | 67 | MANE Select | |
| RefSeq | NP_001177638.1 | 66 | Standard | |
| RefSeq | NP_542196.2 | 67 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein digestion and absorption - Homo sapiens (human)
- Focal Adhesion
- Focal Adhesion-PI3K-Akt-mTOR-signaling pathway
- Collagen chain trimerization
- Collagen biosynthesis and modifying enzymes
Biological Process
- cartilage condensation
- ossification
- chondrocyte development
- proteoglycan metabolic process
- visual perception
Molecular Function
- extracellular matrix structural constituent
- heparin binding
- extracellular matrix structural constituent conferring tensile strength
- protein binding, bridging
- metal ion binding
Cellular Component
- extracellular region
- collagen type XI trimer
- extracellular space
- endoplasmic reticulum lumen
- extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370096
- Coding exons
- 67
- Length
- 232030
- Individuals with no LoFs
- 125708
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 40
- Defined
- 125748
- p
- 0.000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.02 | 903 | 994 | 0.909 | 0.0000503 | 11410 |
| Missense (PolyPhen) | 166 | 183.93 | 0.90251 | 2148 | ||
| Synonymous | -1.26 | 350 | 321 | 1.09 | 0.0000165 | 3744 |
| Loss of Function | 8.61 | 17 | 118 | 0.144 | 0.00000599 | 1433 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00015 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils.;
- Disease
- DISEASE: Stickler syndrome 2 (STL2) [MIM:604841]: An autosomal dominant form of Stickler syndrome, an inherited disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal degeneration, retinal detachment, and chronic uveitis. Pierre Robin sequence includes an opening in the roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome expressivity is variable. {ECO:0000269|PubMed:10486316, ECO:0000269|PubMed:20513134, ECO:0000269|PubMed:8872475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Marshall syndrome (MRSHS) [MIM:154780]: An autosomal dominant disorder characterized by ocular abnormalities, deafness, craniofacial anomalies, and anhidrotic ectodermal dysplasia. Clinical features include short stature; flat or retruded midface with short, depressed nose, flat nasal bridge and anteverted nares; cleft palate with or without the Pierre Robin sequence; appearance of large eyes with ocular hypertelorism; cataracts, either congenital or juvenile; esotropia; high myopia; sensorineural hearing loss; spondyloepiphyseal abnormalities; calcification of the falx cerebri; ectodermal abnormalities, including defects in sweating and dental structures. {ECO:0000269|PubMed:10486316}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Fibrochondrogenesis 1 (FBCG1) [MIM:228520]: A severe short-limbed skeletal dysplasia characterized by broad long-bone metaphyses, pear-shaped vertebral bodies, and characteristic morphology of the growth plate, in which the chondrocytes have a fibroblastic appearance and there are regions of fibrous cartilage extracellular matrix. Clinical features include a flat midface with a small nose and anteverted nares, significant shortening of all limb segments but relatively normal hands and feet, and a small bell-shaped thorax with a protuberant abdomen. {ECO:0000269|PubMed:21035103}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.347
Intolerance Scores
- LoFtool
- 0.00944
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 28.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.222
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |