COL11A1

protein-coding

collagen 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]

Previous symbols:
  • COLL6
  • DFNA37

MANE transcript

NM_001854.4

Inheritance

AD, AR

ClinVar variants

P:283U:1186B:835

Top phenotype

Stickler syndrome, type II; Deafness, autosomal dominant, 37; Fibrochondrogenesis; Marshall syndrome

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr1:102,876,467-103,108,872

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~232.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Marshall syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007949

Submitter: Genomics England PanelApp

hearing loss, autosomal dominant 37MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0032802

Submitter: Ambry Genetics

Stickler syndrome type 2DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011493

Submitter: G2P

autosomal dominant myopia-midfacial retrusion-sensorineural hearing loss-rhizomelic dysplasia syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018601

Submitter: Orphanet

Stickler syndrome type 2SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011493

Submitter: Orphanet

fibrochondrogenesisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016068

Submitter: Orphanet

Marshall syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0007949

Submitter: Genomics England PanelApp

hearing loss, autosomal dominant 37STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032802

Submitter: Labcorp Genetics (formerly Invitae)

Marshall syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007949

Submitter: Labcorp Genetics (formerly Invitae)

Marshall syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0007949

Submitter: G2P

fibrochondrogenesis 1STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009226

Submitter: Labcorp Genetics (formerly Invitae)

autosomal dominant nonsyndromic hearing lossMODERATE

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).

Marshall syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007949

Submitter: Orphanet

Stickler syndrome type 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011493

Submitter: Genomics England PanelApp

fibrochondrogenesis 1DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009226

Submitter: G2P

Stickler syndrome type 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011493

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Stickler syndrome, type II; Deafness, autosomal dominant, 37; Fibrochondrogenesis; Marshall syndromeAD/AR

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

Refs: 13520885; 749746; 6694183; 6507479; 6507478; 8733059; 8872475; 9129742; 10573014; 9529347; 9475607; 10486316; 15286167; 17236192; 21035103; 20301479; 30245514; 33169910; 33605226Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COL11A1 variants in ClinVar

42 Conditions Cataloged
not providedTotal: 2988
not specifiedTotal: 458
COL11A1-related disorderTotal: 327
Stickler syndrome type 2Total: 240
Inborn genetic diseasesTotal: 232
Fibrochondrogenesis 1Total: 159
Marshall syndromeTotal: 89
Hearing loss, autosomal dominant 37Total: 75

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
28
clinvar
423
clinvar
29
clinvar
482
missense
10
clinvar
58
clinvar
1139
clinvar
338
clinvar
45
clinvar
1590
nonsense
20
clinvar
15
clinvar
1
clinvar
36
start loss
0
frameshift
25
clinvar
21
clinvar
4
clinvar
50
splice donor/acceptor (+/-2bp)
36
clinvar
96
clinvar
14
clinvar
146
Total911921186761742304

Highest pathogenic variant AF is 0.00004363048

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001854.4RefSeqNP_001845.367MANE Select
ENST00000370096.9EnsemblENSP00000359114.367MANE Select
NM_001190709.2RefSeqNP_001177638.166Standard
NM_080629.3RefSeqNP_542196.267Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.029039940.9090.000050311410
Missense (PolyPhen)166183.930.902512148
Synonymous-1.263503211.090.00001653744
Loss of Function8.61171180.1440.000005991433

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.000200.00020rare
Ashkenazi Jewish00.0absent
East Asian0.000600.00060rare
Finnish00.0absent
European (Non-Finnish)0.000150.00015rare
South Asian0.000100.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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