COL11A2

gene
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Also known as HKE5

Summary

COL11A2 (collagen type XI alpha 2 chain, HGNC:2187) is a protein-coding gene on chromosome 6p21.32, encoding Collagen alpha-2(XI) chain (P13942). May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils.

This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. It is located on chromosome 6 very close to but separate from the gene for retinoid X receptor beta. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Proteolytic processing of this type XI chain produces PARP, a proline/arginine-rich protein that is an amino terminal domain. Mutations in this gene are associated with type III Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED syndrome), Weissenbacher-Zweymuller syndrome, autosomal dominant non-syndromic sensorineural type 13 deafness (DFNA13), and autosomal recessive non-syndromic sensorineural type 53 deafness (DFNB53). Alternative splicing results in multiple transcript variants. A related pseudogene is located nearby on chromosome 6.

Source: NCBI Gene 1302 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): nonsyndromic genetic hearing loss (Definitive, ClinGen) — +8 more curated relationships
  • GWAS associations: 13
  • Clinical variants (ClinVar): 3,179 total — 109 pathogenic, 70 likely-pathogenic
  • Phenotypes (HPO): 103
  • Druggable target: yes
  • MANE Select transcript: NM_080680

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2187
Approved symbolCOL11A2
Namecollagen type XI alpha 2 chain
Location6p21.32
Locus typegene with protein product
StatusApproved
AliasesHKE5
Ensembl geneENSG00000204248
Ensembl biotypeprotein_coding
OMIM120290
Entrez1302

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000341947, ENST00000361917, ENST00000374708, ENST00000395194, ENST00000477772, ENST00000682718, ENST00000683572, ENST00000930121, ENST00000930122

RefSeq mRNA: 9 — MANE Select: NM_080680 NM_001163771, NM_001424108, NM_001424109, NM_001424110, NM_001424111, NM_001424112, NM_080679, NM_080680, NM_080681

CCDS: CCDS43452, CCDS54992

Canonical transcript exons

ENST00000341947 — 66 exons

ExonStartEnd
ENSE000015919173318025833180332
ENSE000015931423316742633167533
ENSE000015938013316851933168572
ENSE000015972123317401133174055
ENSE000016090333317643333176486
ENSE000016114953318662733186818
ENSE000016149503317350233173555
ENSE000016190603317843533178488
ENSE000016195173317971933179805
ENSE000016261083316672033166827
ENSE000016283183318570133185778
ENSE000016286773316983133169884
ENSE000016375223317625933176303
ENSE000016383953317004733170100
ENSE000016394203317907333179126
ENSE000016448413316593133165984
ENSE000016493963318096433181005
ENSE000016512423317557433175681
ENSE000016546863317171333171820
ENSE000016563293316726433167317
ENSE000016573833317334833173401
ENSE000016579653317830833178352
ENSE000016619933317892033178973
ENSE000016626693316938333169490
ENSE000016628473318932033189469
ENSE000016698973317699233177045
ENSE000016750033317055733170610
ENSE000016830813317370133173745
ENSE000016861463318066833180730
ENSE000016945013317081033170917
ENSE000016955813316895533169008
ENSE000016970523317867933178732
ENSE000017001593316870633168759
ENSE000017005123317111433171167
ENSE000017006063317923133179284
ENSE000017039053317228933172378
ENSE000017111543318897833189188
ENSE000017159283317306033173113
ENSE000017169003317127133171324
ENSE000017209583319215933192467
ENSE000017220473317032633170379
ENSE000017277203317452733174580
ENSE000017343993317205033172103
ENSE000017434513318414533184324
ENSE000017484283318836233188524
ENSE000017505533316707033167123
ENSE000017516033317601633176069
ENSE000017556933317943133179487
ENSE000017608323317416533174218
ENSE000017622153318499233185054
ENSE000017687783316617133166206
ENSE000017693613316779933167852
ENSE000017789273316651333166566
ENSE000017794993317146733171574
ENSE000017842083317387333173926
ENSE000017864613318111133181170
ENSE000017883813317672133176765
ENSE000017884993317253033172637
ENSE000035447223317718133177225
ENSE000035470733317766233177706
ENSE000035512643317741233177465
ENSE000035564563316426733164473
ENSE000035745443316554933165816
ENSE000036344453316485233164964
ENSE000037848843317813233178185
ENSE000038970623316269433163818

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 88.77.

FANTOM5 (CAGE): breadth broad, TPM avg 4.4334 / max 632.0300, expressed in 318 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
731004.1706258
730900.101366
730970.048916
730990.043714
730980.038511
730910.01924
730960.01126

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pituitary glandUBERON:000000788.77gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.70gold quality
adenohypophysisUBERON:000219687.53gold quality
right hemisphere of cerebellumUBERON:001489086.95gold quality
cerebellar hemisphereUBERON:000224586.55gold quality
cerebellar cortexUBERON:000212986.46gold quality
cerebellumUBERON:000203785.82gold quality
C1 segment of cervical spinal cordUBERON:000646981.96gold quality
spinal cordUBERON:000224081.93gold quality
putamenUBERON:000187478.85gold quality
right frontal lobeUBERON:000281078.72gold quality
substantia nigraUBERON:000203877.71gold quality
Ammon’s hornUBERON:000195477.25gold quality
central nervous systemUBERON:000101776.73gold quality
brainUBERON:000095576.55gold quality
Brodmann (1909) area 9UBERON:001354076.32gold quality
caudate nucleusUBERON:000187376.30gold quality
nucleus accumbensUBERON:000188275.89gold quality
left testisUBERON:000453375.80gold quality
right testisUBERON:000453475.48gold quality
primary visual cortexUBERON:000243675.44gold quality
hypothalamusUBERON:000189875.31gold quality
amygdalaUBERON:000187674.89gold quality
testisUBERON:000047374.74gold quality
temporal lobeUBERON:000187174.55gold quality
dorsolateral prefrontal cortexUBERON:000983474.34gold quality
ventricular zoneUBERON:000305374.11gold quality
superior frontal gyrusUBERON:000266173.16gold quality
cortical plateUBERON:000534373.08gold quality
anterior cingulate cortexUBERON:000983572.60gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-GEOD-75367no49.88
E-ANND-3no0.91

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF, ERG, EWSR1, HMGA2, MAF, SOX10, SOX9, SP1, SP3, SP7, ZNF219, ZNF250, ZNF263

miRNA regulators (miRDB)

12 targeting COL11A2, 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-807599.9767.20962
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-806199.6369.441411
HSA-MIR-6752-5P99.5967.321243
HSA-MIR-1224-5P99.4865.59803
HSA-MIR-130A-5P99.3370.262623
HSA-MIR-447899.0765.162320
HSA-MIR-6760-5P98.8766.731515
HSA-MIR-6804-5P98.3965.771084
HSA-MIR-392998.3265.581026
HSA-MIR-3162-5P95.6767.53794

Literature-anchored findings (GeneRIF, showing 29)

  • differential regulation by EWS/ERG sarcoma fusion protein and wild-type ERG (PMID:12554743)
  • sequence variations in these genes can play a role in the etiology of Robin sequence, cleft palate and micrognathia but are not common causes of these phenotypes. (PMID:12673280)
  • Mutation in the COL11A2 gene was found in all affected individuals, which lends molecular support to the clinical notion that autosomal recessive Weissenbacher-Zweymuller syndrome (WZS) and otospondylomegaepiphyseal dysplasia (OSMED)are a single entity. (PMID:15558753)
  • mutation type and location are critical determinants in defining the phenotype of COL11A2 associated diseases (PMID:16033917)
  • COL11A2 transcription is regulated by Sp1 proteins and by binding to its proximal promoter (PMID:16734381)
  • This study is the first to show that collagen XI is present in the Golgi apparatus of normal human colon goblet cells and localizes collagen XI in both normal and malignant tissue. (PMID:18040076)
  • diagnosis ofOtospondylomegaepiphyseal dysplasia was diagnosed by identifying a mutation in the COL11A2 gene that encodes the pre-pro-alpha2(XI) chain of type XI collagen that is involved in type II collagen fibrillogenesis. (PMID:18381781)
  • individuals carrying the C allele at the COL11A2 SNP site, rs2076311, had a lower risk of Kawasaki disease and had a lower probability of developing coronary artery lesions (PMID:20618517)
  • implication of IRF6, COL2A1, and WNT3 in occurrence of nonsyndromic cleft palate (NSCP); likely variation in cartilage collagen II and XI genes, IRF6, and Wnt and FGF signal pathway genes contributes susceptibility to NSCP in Northeast Europe populations (PMID:20672350)
  • A novel homozygous COL11A2 deletion causes a C-terminal protein truncation with incomplete mRNA decay in a Turkish patient. (PMID:21204229)
  • four loci showed the strongest associations with RA (P<0.005): ZNF391, OR2H1, C6orf26-RDBP and HLA-DPB1-COL11A2. (PMID:21293383)
  • The findings of a significant association between lip and/or palate clefts and two markers in the WNT3 and COL11A2 genes were the most consistent and were observed in all groups analysed and stratified. (PMID:22112025)
  • These findings thus demonstrate that fibrochondrogenesis can result from either recessively or dominantly inherited mutations in COL11A2 (PMID:22246659)
  • Hearing impairment in non-ocular Stickler syndrome is characterized by non-progressive hearing loss, present since childhood, and mostly mild to moderate in severity. Heterozygote mutations in COL11A2 were present in two pedigrees. (PMID:22796475)
  • results show that this gene interacts collagen x1 encoded genes to modulate the risk for AT (PMID:23624467)
  • Expanded spectrum of mutations in the COL11A1 and COL11A2 genes in Stickler syndrome. (PMID:25240749)
  • Data indicate that Ala37Ser is the missense mutation located in the NC4 domain of the collagen type XI COL11A2 protein. (PMID:25633957)
  • A novel mutation in COL11A2 was found in a Japanese family with non-ocular Stickler syndrome. (PMID:25780254)
  • Up to now, merely 7 loci have been linked to mid-frequency hearing loss. Only four genetic mid-frequency deafness genes, namely, DFNA10 (EYA4), DFNA8/12 (TECTA), DFNA13 (COL11A2), DFNA44 (CCDC50), have been reported to date. [review] (PMID:27142990)
  • Missense mutations in COL6A1, COL11A2, FGFR1, and BMP2 genetically predispose patients to ossification of posterior longitudinal ligaments. (PMID:27246988)
  • that the COL11A2 gene, which has previously been associated with familial osteoarthritis, may play a role in pain sensitization after the development of osteoarthritis (PMID:28741447)
  • Mutation in COL11A2 gene is associated with Stargardt disease as well as Stickler’s Syndrome . (PMID:30156925)
  • rs986522(C) significantly increased the risk of lumbar disc degeneration in Chinese Han females. (PMID:30548218)
  • Genetic variant of COL11A2 gene is functionally associated with developmental dysplasia of the hip in Chinese Han population. (PMID:32396528)
  • Exon-Trapping Assay Improves Clinical Interpretation of COL11A1 and COL11A2 Intronic Variants in Stickler Syndrome Type 2 and Otospondylomegaepiphyseal Dysplasia. (PMID:33348901)
  • Association Between COL5a1, COL11a1, and COL11a2 Gene Variations and Rotator Cuff Tendinopathy in Young Athletes. (PMID:34009784)
  • The Association of Variants within Types V and XI Collagen Genes with Knee Joint Laxity Measurements. (PMID:36553626)
  • COL11A2 as a candidate gene for vertebral malformations and congenital scoliosis. (PMID:37462524)
  • Autosomal recessive otospondylo-mega-epiphyseal dysplasia: comprehensive clinical review of a pediatric cohort. (PMID:37646720)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocol11a2ENSDARG00000012422
mus_musculusCol11a2ENSMUSG00000024330
rattus_norvegicusCol11a2ENSRNOG00000000463

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), COL6A2 (ENSG00000142173), 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), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

Collagen alpha-2(XI) chainP13942 (reviewed: P13942)

All UniProt accessions (4): P13942, A0A0C4DFS1, H0YIS1, Q4VXY6

UniProt curated annotations — full annotation on UniProt →

Function. May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils.

Subunit / interactions. Trimers composed of three different chains: alpha 1(XI), alpha 2(XI), and alpha 3(XI). Alpha 3(XI) is a post-translational modification of alpha 1(II). Alpha 1(V) can also be found instead of alpha 3(XI)=1(II).

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

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. A disulfide-bonded peptide called proline/arginine-rich protein or PARP is released from the N-terminus during extracellular processing and is subsequently retained in the cartilage matrix from which it can be isolated in significant amounts.

Disease relevance. Otospondylomegaepiphyseal dysplasia, autosomal dominant (OSMEDA) [MIM:184840] An autosomal dominant form of otospondylomegaepiphyseal dysplasia, a disorder characterized by sensorineural deafness, enlarged epiphyses, mild platyspondyly, and disproportionate shortness of the limbs. Total body length is normal. Typical facial features are mid-face hypoplasia, short upturned nose and depressed nasal bridge. Most patients have Pierre Robin sequence including an opening in the roof of the mouth (cleft palate) and a small lower jaw (micrognathia). Ocular symptoms are absent. Some patients have early-onset osteoarthritis. The disease is caused by variants affecting the gene represented in this entry. Otospondylomegaepiphyseal dysplasia, autosomal recessive (OSMEDB) [MIM:215150] An autosomal recessive form of otospondylomegaepiphyseal dysplasia, a disorder characterized by sensorineural deafness, enlarged epiphyses, mild platyspondyly, and disproportionate shortness of the limbs. Total body length is normal. Typical facial features are mid-face hypoplasia, short upturned nose and depressed nasal bridge. Most patients have Pierre Robin sequence including an opening in the roof of the mouth (cleft palate) and a small lower jaw (micrognathia). Ocular symptoms are absent. Some patients have early-onset osteoarthritis. The disease is caused by variants affecting the gene represented in this entry. Deafness, autosomal dominant, 13 (DFNA13) [MIM:601868] A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. The disease is caused by variants affecting the gene represented in this entry. Deafness, autosomal recessive, 53 (DFNB53) [MIM:609706] A form of non-syndromic sensorineural deafness characterized by prelingual, profound, non-progressive hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. The disease is caused by variants affecting the gene represented in this entry. Fibrochondrogenesis 2 (FBCG2) [MIM:614524] A severe skeletal dysplasia characterized by a flat midface, short long bones, short ribs with broad metaphyses, and vertebral bodies that show distinctive hypoplastic posterior ends and rounded anterior ends, giving the vertebral bodies a pinched appearance on lateral radiographic views. The chest is small, causing perinatal respiratory problems which usually, but not always, result in lethality. Affected individuals who survive the neonatal period have high myopia, mild to moderate hearing loss, and severe skeletal dysplasia. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function.

Similarity. Belongs to the fibrillar collagen family.

Isoforms (9)

UniProt IDNamesCanonical?
P13942-11yes
P13942-22
P13942-33
P13942-44
P13942-55
P13942-66
P13942-77
P13942-88
P13942-99

RefSeq proteins (9): NP_001157243, NP_001411037, NP_001411038, NP_001411039, NP_001411040, NP_001411041, NP_542410, NP_542411, NP_542412 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000885Fib_collagen_CDomain
IPR001791Laminin_GDomain
IPR008160CollagenRepeat
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR048287TSPN-like_NDomain
IPR050149Collagen_superfamilyFamily

Pfam: PF01391, PF01410, PF02210

UniProt features (95 total): compositionally biased region 23, sequence variant 19, sequence conflict 19, domain 10, region of interest 5, binding site 5, disulfide bond 5, splice variant 5, signal peptide 1, chain 1, propeptide 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P13942-F150.180.13

Functional residue map

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

Ligand- & substrate-binding residues (5): 1589; 1591; 1592; 1594; 1597

Disulfide bonds (5): 1571–1603, 1577, 1594, 1612–1733, 1655–1689

Glycosylation sites (1): 1604

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-1442490Collagen degradation
R-HSA-1650814Collagen biosynthesis and modifying enzymes
R-HSA-2022090Assembly of collagen fibrils and other multimeric structures
R-HSA-3000171Non-integrin membrane-ECM interactions
R-HSA-8874081MET activates PTK2 signaling
R-HSA-8948216Collagen chain trimerization
R-HSA-9925563Developmental Lineage of Pancreatic Ductal Cells

MSigDB gene sets: 417 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, CREL_01, CHIBA_RESPONSE_TO_TSA_UP, GOBP_COLLAGEN_FIBRIL_ORGANIZATION, GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOCC_COLLAGEN_TRIMER, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, AP2_Q3, GGGTGGRR_PAX4_03, NKX61_01, NFKB_C, IRF7_01

GO Biological Process (9): skeletal system development (GO:0001501), sensory perception of sound (GO:0007605), collagen fibril organization (GO:0030199), cartilage development (GO:0051216), roof of mouth development (GO:0060021), soft palate development (GO:0060023), tissue homeostasis (GO:0001894), chondrocyte differentiation (GO:0002062), skeletal system morphogenesis (GO:0048705)

GO Molecular Function (5): extracellular matrix structural constituent conferring tensile strength (GO:0030020), protein-macromolecule adaptor activity (GO:0030674), metal ion binding (GO:0046872), extracellular matrix structural constituent (GO:0005201), protein binding (GO:0005515)

GO Cellular Component (7): extracellular region (GO:0005576), collagen type II trimer (GO:0005585), collagen type XI trimer (GO:0005592), endoplasmic reticulum lumen (GO:0005788), extracellular matrix (GO:0031012), collagen trimer (GO:0005581), ribosome (GO:0005840)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Collagen formation2
Degradation of the extracellular matrix1
Extracellular matrix organization1
MET promotes cell motility1
Collagen biosynthesis and modifying enzymes1
Developmental Cell Lineages of the Exocrine Pancreas1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
skeletal system development2
anatomical structure development2
fibrillar collagen trimer2
system development1
sensory perception of mechanical stimulus1
extracellular matrix organization1
animal organ development1
connective tissue development1
secondary palate development1
multicellular organismal-level homeostasis1
anatomical structure homeostasis1
cell differentiation1
cartilage development1
animal organ morphogenesis1
extracellular matrix structural constituent1
protein binding1
molecular adaptor activity1
cation binding1
structural molecule activity1
extracellular matrix1
binding1
cellular anatomical structure1
endoplasmic reticulum1
intracellular organelle lumen1
external encapsulating structure1
protein-containing complex1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1562 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
COL11A2LHFPL5Q8TAF8856
COL11A2COL2A1P02458840
COL11A2RXRBP28702804
COL11A2HSD17B8Q92506798
COL11A2KIFC1Q9BW19795
COL11A2RGL2O15211786
COL11A2RPS18P25232786
COL11A2SLC39A7Q92504780
COL11A2PFDN6O15212702
COL11A2HAPLN1P10915680
COL11A2RING1Q06587660
COL11A2PCOLCEQ15113636
COL11A2COL5A1P20908622
COL11A2MIAQ16674608
COL11A2LHFPL3Q86UP9605

IntAct

9 interactions, top by confidence:

ABTypeScore
COL11A2DDR2psi-mi:“MI:0407”(direct interaction)0.560
DDR2COL11A2psi-mi:“MI:0407”(direct interaction)0.560
COL11A2RPL9psi-mi:“MI:0915”(physical association)0.400
COL11A2ANXA7psi-mi:“MI:0915”(physical association)0.370
COL11A2PIN1psi-mi:“MI:0915”(physical association)0.370
TK1COL11A2psi-mi:“MI:0915”(physical association)0.370
WDR20POLR1Cpsi-mi:“MI:0914”(association)0.350
LTKAIPpsi-mi:“MI:2364”(proximity)0.270

BioGRID (12): RPL9 (Proximity Label-MS), COL11A2 (Affinity Capture-RNA), COL11A2 (PCA), COL11A2 (Proximity Label-MS), COL11A2 (Cross-Linking-MS (XL-MS)), COL11A2 (Affinity Capture-MS), COL11A2 (Affinity Capture-MS), COL11A2 (Co-fractionation), COL11A2 (Affinity Capture-MS), COL11A2 (Two-hybrid), COL11A2 (Two-hybrid), COL11A2 (Two-hybrid)

ESM2 similar proteins: A0A060WQA3, A0MSJ1, A5PN28, A6NHN0, A8WGB1, A8WR59, B2RNN3, B7Z0K8, C7DZK3, O35167, O35348, O76368, O88207, P0C862, P12107, P13942, P20908, P20909, P23805, P25067, P25318, P25940, P42916, P83371, P98085, Q03637, Q07092, Q07563, Q0II24, Q0VF58, Q17RW2, Q30D77, Q32S24, Q3MI99, Q4ZJM7, Q4ZJN1, Q60467, Q61245, Q64739, Q6UXH8

Diamond homologs: A0MSJ1, C7DZK3, O42350, O88207, P02452, P02457, P02458, P02459, P02460, P02461, P02466, P05997, P08121, P12105, P12107, P13941, P13942, P20908, P20909, Q17RW2, Q30D77, Q32S24, Q3U962, Q5QNQ9, Q60467, Q61245, Q64739, Q6P4Z2, Q80ZF0, Q8IZC6, Q91717, Q9JI03, Q9YIB4, B8V7R6, O46392, O93484, P02453, P02454, P02465, P02467

SIGNOR signaling

1 interactions.

AEffectBMechanism
SOX9“up-regulates quantity by expression”COL11A2“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

3179 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic109
Likely pathogenic70
Uncertain significance1012
Likely benign1464
Benign126

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1252015NM_080680.3(COL11A2):c.1871dup (p.Gly625fs)Pathogenic
1322103NM_080680.3(COL11A2):c.328C>T (p.Arg110Ter)Pathogenic
1322104NM_080680.3(COL11A2):c.2540del (p.Gly847fs)Pathogenic
1351259NM_080680.3(COL11A2):c.4265dup (p.Gly1423_Glu1424insTer)Pathogenic
1357508NM_080680.3(COL11A2):c.3545del (p.Pro1182fs)Pathogenic
1371095NM_080680.3(COL11A2):c.272G>A (p.Arg91Gln)Pathogenic
1379760NM_080680.3(COL11A2):c.1957del (p.Thr653fs)Pathogenic
1402330NM_080680.3(COL11A2):c.3496G>T (p.Glu1166Ter)Pathogenic
1451542NM_080680.3(COL11A2):c.3032del (p.Pro1011fs)Pathogenic
1452394NM_080680.3(COL11A2):c.4519C>T (p.Gln1507Ter)Pathogenic
1459216NM_080680.3(COL11A2):c.1636C>T (p.Arg546Ter)Pathogenic
160366NM_080680.3(COL11A2):c.109G>T (p.Ala37Ser)Pathogenic
1701500NM_080680.3(COL11A2):c.4123-1G>TPathogenic
1708726NM_080680.3(COL11A2):c.3133G>T (p.Gly1045Ter)Pathogenic
17120NM_080680.3(COL11A2):c.4392+1G>APathogenic
17122NM_080680.3(COL11A2):c.2822_2848del (p.Glu941_Pro950delinsAla)Pathogenic
17123NM_080680.3(COL11A2):c.4322G>A (p.Gly1441Glu)Pathogenic
17125NM_080680.3(COL11A2):c.2423G>A (p.Gly808Glu)Pathogenic
17126NM_080680.3(COL11A2):c.2492C>A (p.Ser831Ter)Pathogenic
17128NM_080680.3(COL11A2):c.3991C>T (p.Arg1331Ter)Pathogenic
17130NM_080680.3(COL11A2):c.3962delPathogenic
1804120NM_080680.3(COL11A2):c.2086del (p.Glu696fs)Pathogenic
1951094NM_080680.3(COL11A2):c.874C>T (p.Gln292Ter)Pathogenic
1975014NM_080680.3(COL11A2):c.1672C>T (p.Arg558Ter)Pathogenic
2022159NM_080680.3(COL11A2):c.2658del (p.Pro888fs)Pathogenic
2022530NM_080680.3(COL11A2):c.1962del (p.Thr656fs)Pathogenic
2098356NM_080680.3(COL11A2):c.3833dup (p.Gly1279fs)Pathogenic
2117536NM_080680.3(COL11A2):c.1586del (p.Gly529fs)Pathogenic
2118997NM_080680.3(COL11A2):c.1076_1077del (p.Glu359fs)Pathogenic
2130254NM_080680.3(COL11A2):c.966del (p.Thr323fs)Pathogenic

SpliceAI

6632 predictions. Top by Δscore:

VariantEffectΔscore
6:33163815:GTGT:Gacceptor_gain1.0000
6:33163817:GT:Gacceptor_gain1.0000
6:33163819:C:CAacceptor_loss1.0000
6:33163819:C:CCacceptor_gain1.0000
6:33163822:C:CTacceptor_gain1.0000
6:33163823:A:Tacceptor_gain1.0000
6:33164255:T:TAdonor_gain1.0000
6:33164261:TCCCA:Tdonor_loss1.0000
6:33164262:CCCAC:Cdonor_loss1.0000
6:33164263:CCACC:Cdonor_loss1.0000
6:33164264:CACCT:Cdonor_loss1.0000
6:33164265:A:Tdonor_loss1.0000
6:33164266:CCTG:Cdonor_loss1.0000
6:33164317:G:Cdonor_gain1.0000
6:33164321:AT:Adonor_gain1.0000
6:33164322:T:TAdonor_gain1.0000
6:33164388:T:TAdonor_gain1.0000
6:33164469:GAGAA:Gacceptor_gain1.0000
6:33164470:AGAA:Aacceptor_gain1.0000
6:33164471:GAA:Gacceptor_gain1.0000
6:33164472:AA:Aacceptor_gain1.0000
6:33164472:AAC:Aacceptor_loss1.0000
6:33164473:AC:Aacceptor_loss1.0000
6:33164474:C:CCacceptor_gain1.0000
6:33164474:C:Tacceptor_loss1.0000
6:33164475:T:Cacceptor_loss1.0000
6:33164847:CTCAC:Cdonor_loss1.0000
6:33164850:A:ACdonor_gain1.0000
6:33164851:C:CCdonor_gain1.0000
6:33164851:CCTG:Cdonor_gain1.0000

AlphaMissense

10817 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:33164906:G:CC1603W1.000
6:33164907:C:GC1603S1.000
6:33164907:C:TC1603Y1.000
6:33164908:A:GC1603R1.000
6:33164908:A:TC1603S1.000
6:33165578:A:GL1574P1.000
6:33165586:G:CC1571W1.000
6:33165587:C:TC1571Y1.000
6:33163688:A:CF1734C0.999
6:33163688:A:GF1734S0.999
6:33164405:G:CS1644R0.999
6:33164405:G:TS1644R0.999
6:33164407:T:GS1644R0.999
6:33164412:A:GL1642P0.999
6:33164420:G:CF1639L0.999
6:33164420:G:TF1639L0.999
6:33164421:A:CF1639C0.999
6:33164422:A:GF1639L0.999
6:33164907:C:AC1603F0.999
6:33164942:G:CN1591K0.999
6:33164942:G:TN1591K0.999
6:33164946:G:TP1590H0.999
6:33164949:T:CD1589G0.999
6:33164959:A:CY1586D0.999
6:33165587:C:AC1571F0.999
6:33165587:C:GC1571S0.999
6:33165588:A:GC1571R0.999
6:33165588:A:TC1571S0.999
6:33166799:C:TG1420E0.999
6:33166808:C:TG1417E0.999

dbSNP variants (sampled 300 via entrez): RS1000091006 (6:33181588 C>T), RS1000116715 (6:33188793 A>C), RS1000174480 (6:33162309 A>G), RS1000260021 (6:33175499 C>T), RS1000355634 (6:33168444 A>C), RS1000411560 (6:33175880 G>A), RS1000420177 (6:33181953 G>A), RS1000491541 (6:33194538 G>C,T), RS1000612226 (6:33194223 A>G), RS1000892992 (6:33176659 C>T), RS1001105186 (6:33187567 A>G), RS1001125057 (6:33190663 G>A), RS1001222814 (6:33188872 G>A), RS1001257347 (6:33181334 C>A,T), RS1001309151 (6:33187917 G>A)

Disease associations

OMIM: gene MIM:120290 | disease phenotypes: MIM:215150, MIM:601868, MIM:184840, MIM:277610, MIM:609706, MIM:614524, MIM:241500, MIM:245600, MIM:128600, MIM:257350, MIM:257850, MIM:614211, MIM:190685

GenCC curated gene-disease

DiseaseClassificationInheritance
otospondylomegaepiphyseal dysplasia, autosomal dominantDefinitiveAutosomal dominant
otospondylomegaepiphyseal dysplasia, autosomal recessiveDefinitiveAutosomal recessive
autosomal dominant nonsyndromic hearing loss 13DefinitiveAutosomal dominant
autosomal recessive nonsyndromic hearing loss 53DefinitiveAutosomal recessive
otospondylomegaepiphyseal dysplasiaDefinitiveAutosomal dominant
fibrochondrogenesisSupportiveAutosomal dominant
autosomal dominant nonsyndromic hearing lossSupportiveAutosomal dominant
hearing loss, autosomal recessiveSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (4)

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

DiseaseClassificationInheritance
nonsyndromic genetic hearing lossDefinitiveAD
otospondylomegaepiphyseal dysplasiaDefinitiveAD
otospondylomegaepiphyseal dysplasiaDefinitiveAR
nonsyndromic genetic hearing lossModerateAR

Mondo (23): otospondylomegaepiphyseal dysplasia, autosomal recessive (MONDO:0044206), autosomal dominant nonsyndromic hearing loss 13 (MONDO:0011159), hearing loss disorder (MONDO:0005365), otospondylomegaepiphyseal dysplasia, autosomal dominant (MONDO:0008490), autosomal recessive nonsyndromic hearing loss 53 (MONDO:0012333), fibrochondrogenesis 2 (MONDO:0013795), infantile hypophosphatasia (MONDO:1010169), connective tissue disorder (MONDO:0003900), Larsen-like syndrome, B3GAT3 type (MONDO:0009511), nonsyndromic genetic hearing loss (MONDO:0019497), conductive hearing loss disorder (MONDO:0020679), sensorineural hearing loss disorder (MONDO:0020678), ear malformation (MONDO:0007500), cystic hygroma (MONDO:0009761), oculodentodigital dysplasia, autosomal recessive (MONDO:0009768)

Orphanet (16): Autosomal recessive otospondylomegaepiphyseal dysplasia (Orphanet:1427), Rare autosomal dominant non-syndromic sensorineural deafness type DFNA (Orphanet:90635), Autosomal dominant otospondylomegaepiphyseal dysplasia (Orphanet:166100), Fibrochondrogenesis (Orphanet:2021), Weissenbacher-Zweymuller syndrome (Orphanet:3450), Rare autosomal recessive non-syndromic sensorineural deafness type DFNB (Orphanet:90636), Infantile hypophosphatasia (Orphanet:247651), Hypophosphatasia (Orphanet:436), Rare genetic deafness (Orphanet:96210), Larsen-like syndrome, B3GAT3 type (Orphanet:284139), Rare non-syndromic genetic deafness (Orphanet:87884), Oculodentodigital dysplasia (Orphanet:2710), OBSOLETE: Inherited retinal disorder (Orphanet:71862), Down syndrome (Orphanet:870), Cystic hygroma (Orphanet:79486)

HPO phenotypes

103 total (30 of 103 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000160Narrow mouth
HP:0000162Glossoptosis
HP:0000175Cleft palate
HP:0000193Bifid uvula
HP:0000201Pierre-Robin sequence
HP:0000260Wide anterior fontanel
HP:0000272Malar flattening
HP:0000311Round face
HP:0000316Hypertelorism
HP:0000336Prominent supraorbital ridges
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000358Posteriorly rotated ears
HP:0000364Hearing abnormality
HP:0000369Low-set ears
HP:0000407Sensorineural hearing impairment
HP:0000410Mixed hearing impairment
HP:0000414Bulbous nose
HP:0000463Anteverted nares
HP:0000470Short neck
HP:0000478Abnormality of the eye
HP:0000486Strabismus
HP:0000494Downslanted palpebral fissures
HP:0000518Cataract
HP:0000520Proptosis
HP:0000540Hypermetropia
HP:0000541Retinal detachment
HP:0000767Pectus excavatum

GWAS associations

13 associations (top):

StudyTraitp-value
GCST001613_18Antineutrophil cytoplasmic antibody-associated vasculitis1.000000e-71
GCST002160_5Wegener’s granulomatosis2.000000e-50
GCST002217_5Sjögren’s syndrome9.000000e-25
GCST004748_119Lung cancer1.000000e-06
GCST005790_68Rosacea symptom severity2.000000e-07
GCST007797_34Asthma onset (childhood vs adult)4.000000e-06
GCST007798_48Asthma4.000000e-14
GCST007800_17Asthma (childhood onset)3.000000e-17
GCST008053_72Height3.000000e-13
GCST008365_16Thyrotoxic hypokalemic periodic paralysis and Graves disease2.000000e-18
GCST90020028_532Hip circumference adjusted for BMI8.000000e-09
GCST90020028_533Hip circumference adjusted for BMI5.000000e-10
GCST90020028_534Hip circumference adjusted for BMI2.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0009180rosacea severity measurement
EFO:0004847age at onset
EFO:0008039BMI-adjusted hip circumference

MeSH disease descriptors (15)

DescriptorNameTree numbers
D003240Connective Tissue DiseasesC17.300
D004314Down SyndromeC10.597.606.360.220; C16.131.077.327; C16.131.260.260; C16.320.180.260
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D018191Lymphangioma, CysticC04.557.375.450.450
D058499Retinal DystrophiesC11.768.585.658
C566612Deafness, Autosomal Dominant 13 (supp.)
C564609Deafness, Autosomal Recessive (supp.)
C566453Deafness, Autosomal Recessive 53 (supp.)
C562524Fibrochondrogenesis (supp.)
C537874Larsen syndrome, recessive type (supp.)
C580334Nonsyndromic Deafness (supp.)
C567605Oculodentodigital Dysplasia, Autosomal Recessive (supp.)
C535776Pierre Robin syndrome with fetal chondrodysplasia (supp.)
C537494Stickler syndrome, type 3 (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

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression4
trichostatin Aaffects cotreatment, increases expression3
Cisplatinaffects cotreatment, affects expression, affects response to substance2
aristolochic acid Iincreases expression1
bisphenol Faffects cotreatment, decreases methylation1
triphenyl phosphateaffects expression1
bisphenol Adecreases methylation1
sodium arseniteincreases expression1
benzo(e)pyreneincreases methylation1
tamibaroteneaffects expression1
CGP 52608affects binding, increases reaction1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, increases methylation1
theaflavin-3,3’-digallateaffects expression1
Fulvestrantaffects cotreatment, decreases methylation, increases methylation1
Vorinostataffects cotreatment, increases expression1
Glyphosateincreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, increases methylation1
Doxorubicindecreases expression1
Methapyrileneincreases methylation1
Tamoxifenincreases expression1
Tretinoindecreases expression1
Triclosandecreases expression1
2,4-Dichlorophenoxyacetic Acidincreases expression1
Aflatoxin B1increases methylation1
Paclitaxelaffects expression, affects cotreatment1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)
NCT02832128PHASE2COMPLETEDEvaluating Possible Improvement in Speech and Hearing Tests After 28 Days of Dosing of the Study Drug AUT00063 Compared to Placebo (QuicKfire)
NCT04915183PHASE2RECRUITINGAtorvastatin to Reduce Cisplatin-Induced Hearing Loss Among Individuals With Head and Neck Cancer
NCT05258773PHASE2COMPLETEDEvaluation of the Presence of SENS-401 in the Perilymph
NCT06340633PHASE2RECRUITINGSPI-1005 in Adults Receiving Cochlear Implant
NCT00582946PHASE1COMPLETEDWide-Bandwidth Open Canal Hearing Aid For Better Multitalker Speech Understanding
NCT00584155PHASE1WITHDRAWNProtection From Cisplatin Ototoxicity by Lactated Ringers
NCT01206829PHASE1UNKNOWNHearing Impairment, Cognitive Therapy and Coping
NCT01256229PHASE1COMPLETEDOutcomes In Children With Developmental Delay And Deafness
NCT01343394PHASE1WITHDRAWNSafety of Autologous Human Umbilical Cord Blood Mononuclear Fraction to Treat Acquired Hearing Loss in Children
NCT01452607PHASE1COMPLETEDStudy to Evaluate the Safety and Pharmacokinetics of SPI-1005
NCT02259595PHASE1COMPLETEDStudy to Determine the Safety, Tolerability, and Pharmacokinetic Profile of HPN-07 and HPN-07 Plus NAC
NCT04041440PHASE1COMPLETEDSpeech Recognition Training in Children With Hearing Loss
NCT07218913PHASE1RECRUITINGTesting the Addition of Pedmark to Cisplatin Chemotherapy for Reducing Drug-Induced Ear Damage in Men With Stage II-III Metastatic Testicular Germ Cell Tumors
NCT00486577PHASE2/PHASE3COMPLETEDChronic Electrical Stimulation of the Auditory Cortex for Intractable Tinnitus
NCT00789061PHASE2/PHASE3UNKNOWNApplying Proton Pump Inhibitor to Prevent and Treat Acute Fluctuating Hearing Loss in Patients With SLC26A4 Mutation
NCT01423409PHASE2/PHASE3COMPLETEDMulticenter Trial Assessing an Innovative VAS of Pain Among Deaf People
NCT05786378PHASE2/PHASE3UNKNOWNAssessment of The Efficacy of Intratympanic Platelet Rich Plasma for Treatment of Sensorineural Hearing Loss.
NCT01108601PHASE1/PHASE2UNKNOWNTranstympanic Ringer’s Lactate for the Prevention of Cisplatin Ototoxicity
NCT01621256PHASE1/PHASE2COMPLETEDEfficacy, Safety, and Tolerability of Ancrod in Patients With Sudden Hearing Loss
NCT06370351PHASE1/PHASE2RECRUITINGA Phase I/II Clinical Trial with SENS-501 in Children Suffering from Severe to Profound Hearing Loss Due to Otoferlin (OTOF) Mutations
NCT06545175PHASE1/PHASE2RECRUITINGIntracochlear Application of VSF1.01 for the Reduction of Cochlear Implant Surgery Related Trauma
NCT07304024PHASE1/PHASE2RECRUITINGA Treatment for a Form of Age-Related Central Auditory Processing Disorder Consisting of Clemastine Fumarate Plus Engineered Sound
NCT01109576EARLY_PHASE1COMPLETEDWorkshops for Veterans With Vision and Hearing Loss