COL9A1 - collagen type IX alpha 1 chain Gene

Also Known as MED; EDM6; STL4; DJ149L1.1.2

Species: Homo sapiens

Gene Type: protein coding

Gene ID: 1297

About COL9A1

Cytogenetic location: 6q13 Genomic coordinates (GRCh38): 6:70,215,061-70,303,084 (from NCBI)

This gene has 16 transcripts (splice variants), 198 orthologues, 37 paralogues and is associated with 7 phenotypes. Biased expression in prostate (RPKM 6.1), testis (RPKM 1.3) and 6 other tissues.

Summary

This gene encodes one of the three alpha chains of type IX Collagen, which is a minor (5-20%) Collagen component of hyaline cartilage. Type IX Collagen is usually found in tissues containing type II Collagen, a fibrillar Collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX Collagen molecules, a heterotrimeric molecule, and that lack of type IX Collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

COL9A1 Products (5)

mRNA	Protein	Name
NM_001377289.1	NP_001364218.1	collagen alpha-1(IX) chain isoform 3 precursor
NM_001377290.1	NP_001364219.1	collagen alpha-1(IX) chain isoform 4 precursor
NM_001377291.1	NP_001364220.1	collagen alpha-1(IX) chain isoform 5 precursor
NM_001851.6	NP_001842.3	collagen alpha-1(IX) chain isoform 1 precursor
NM_078485.4	NP_511040.2	collagen alpha-1(IX) chain isoform 2 precursor

Gene Ontology

Molecular Function
Cellular Component

Molecular Function GO Annotation	Evidence	References	Source
enables carbohydrate binding	EXP EXP: Inferred from Experiment	15047691	GOA
enables carbohydrate binding	IMP IMP: Inferred from mutant phenotype	15047691	GOA
enables carbohydrate binding	IPI IPI: Inferred from physical interaction	15047691	GOA
enables protein binding	IPI IPI: Inferred from physical interaction	15047691	GOA
enables protein homodimerization activity	IPI IPI: Inferred from physical interaction	8660302	GOA

Cellular Component GO Annotation	Evidence	References	Source
part of collagen type IX trimer	IDA IDA: Inferred from direct assay	8660302	GOA
part of collagen type IX trimer	IPI IPI: Inferred from physical interaction	27897211	GOA

EXP: Inferred from Experiment IDA: Inferred from direct assay IPI: Inferred from physical interaction IMP: Inferred from mutant phenotype IGI: Inferred from genetic interaction IEP: Inferred from expression pattern

COL9A1 Protein Structure

Collagen

0
200
400
600
800
921 a.a.

Protein Preferred Names	Protein Names
collagen alpha-1(IX) chain	alpha-1(IX) collagen chain

COL9A1 Protein-protein interaction Information

Type	Protein Name	Protein ID	Interactor	Interactor Species	Interactor ID	Detection Method	References
Intra	COL9A1	P20849	COL6A1	Homo sapiens	P12109	Anti Tag CoIP	33961781
Intra	COL9A1	P20849	GIPC1	Homo sapiens	O14908-2	Y2H Array	32814053
Intra	COL9A1	P20849	GIPC1	Homo sapiens	O14908-2	Validated Y2H	32814053
Intra	COL9A1	P20849	GIPC1	Homo sapiens	O14908-2	Y2H Pooling	32814053

Cross: Cross-species interaction Intra: Intraspecies interaction

Recombinant COL9A1 Proteins

Cat. No.	Product Name	Accession	Purity
HY-P70009	Collagen alpha-1(IX) chain/COL9A1 Protein, Human (HEK293, His)	P20849-3 (A24-P328)	≥ 95%, as determined by reducing SDS-PAGE.

Related Diseases

Diseases	Alias
Epiphyseal Dysplasia, Multiple, 6	Multiple Epiphyseal Dysplasia 6 EDM6 Dysplasia, Epiphyseal, Multiple, Type 6
Stickler Syndrome, Type Iv	STL4 Stickler Syndrome, Type 4 Stickler Syndrome 4
Connective Tissue Disease	Connective Tissue Diseases Connective Tissue Disorder Abnormality Of Connective Tissue Disorder Of Connective Tissue Connective Tissue Disorders
Multiple Epiphyseal Dysplasia Due To Collagen 9 Anomaly
Autosomal Recessive Stickler Syndrome
Sensorineural Hearing Loss	Sensory Hearing Loss Sensorineural Deafness Sensorineural Hearing Loss Disorder Hearing Loss, Sensorineural Central Hearing Loss High Frequency Deafness High Frequency Hearing Loss High-Frequency Hearing Loss Perceptive Deafness Perceptive Hearing Loss Perceptive Hearing Loss Or Deafness Hearing Loss Sensorineural Deafness Sensorineural Hearing Loss High-Frequency Hearing Loss, Central Hearing Loss, High-Frequency
Multiple Epiphyseal Dysplasia	Med Polyepiphyseal Dysplasia Edm Epiphyseal Dysplasia, Multiple, 1 Epiphyseal Dysplasia, Multiple, 2 Epiphyseal Dysplasia, Multiple, 3 Epiphyseal Dysplasia, Multiple, 4 Epiphyseal Dysplasia, Multiple, 5 Epiphyseal Dysplasia, Multiple Edm1 Edm2 Edm3 Edm4 Edm5 Epiphyseal Dysplasia, Fairbank Type Epiphyseal Dysplasia, Ribbing Type Multiple Epiphyseal Dysplasia, Autosomal Dominant Multiple Epiphyseal Dysplasia, Autosomal Recessive Rmed Dysplasia, Epiphyseal, Multiple Osteochondrodysplasias
Stickler Syndrome	Arthroophthalmopathy Hereditary Arthro-Ophthalmo-Dystrophy Hereditary Arthro-Ophthalmopathy Stickler Dysplasia Hereditary Progressive Arthroophthalmopathy Stickler Syndrome, Type 1
Pseudoachondroplasia	PSACH Pseudoachondroplastic Dysplasia Pseudoachondroplastic Spondyloepiphyseal Dysplasia Syndrome Spondyloepiphyseal Dysplasia, Pseudoachondroplastic Pseudoachondroplastic Spondyloepiphyseal Dysplasia Spondyloepiphyseal Dysplasia Pseudoachondroplastic
Osteochondritis Dissecans	Osteochondritis Ocd Konig Disease
Osteoarthritis	Osteoarthrosis Degenerative Joint Disease Hypertrophic Arthritis Arthropathy Degenerative Polyarthritis Degenerative Arthritis Osteoarthrosis And Allied Disorder Arthritis, Degenerative Oa Osteoarthritis Deformans Osteoarthrosis Deformans Kashin-Beck Disease
Spinal Stenosis	Lumbar Spinal Stenosis Cervical Spinal Stenosis Spinal Stenosis Of Lumbar Region Spinal Stenosis In Cervical Region Spinal Canal Stenosis
Vitreous Syneresis	Vitreous Degeneration
Marshall Syndrome	MRSHS Deafness, Myopia, Cataract, Saddle Nose-Marshall Type Periodic Fever, Aphthous Stomatitis, Pharyngitis And Adenitis Pfapa Syndrome Pfapa Marshall Syndrome With Periodic Fever Periodic Fever-Aphtous Stomatitis-Pharyngitis-Adenopathy Syndrome
Epiphyseal Dysplasia, Multiple, 2	EDM2 Multiple Epiphyseal Dysplasia 2 Dysplasia, Epiphyseal, Multiple, Type 2
Epiphyseal Dysplasia, Multiple, 4	EDM4 Multiple Epiphyseal Dysplasia 4 Multiple Epiphyseal Dysplasia With Clubfoot Multiple Epiphyseal Dysplasia Type 4 Multiple Epiphyseal Dysplasia, Autosomal Recessive Multiple Epiphyseal Dysplasia With Bilayered Patellae Med4 Polyepiphyseal Dysplasia Type 4 Rmed Autosomal Recessive Multiple Epiphyseal Dysplasia Multiple Epiphyseal Dysplasia With Bilateral Patellae Epiphyseal Dysplasia Multiple 4 Multiple Epiphyseal Dysplasia With Double-Layered Patella Dysplasia, Epiphyseal, Multiple, Type 4
Epiphyseal Dysplasia, Multiple, 5	EDM5 Multiple Epiphyseal Dysplasia 5 Bhmed Multiple Epiphyseal Dysplasia Type 5 Multiple Epiphyseal Dysplasia, Matn3-Related Microepiphyseal Dysplasia, Bilateral Hereditary Bilateral Hereditary Microepiphyseal Dysplasia Multiple Epiphyseal Dysplasia Matn3-Related Epiphyseal Dysplasia Multiple 5 Multiple Epiphyseal Dysplasia, Matn3 Related Bilateral Hereditary Micro-Epiphyseal Dysplasia Med5 Polyepiphyseal Dysplasia Type 5 Dysplasia, Epiphyseal, Multiple, Type 5
Kniest Dysplasia	Kniest Syndrome Metatropic Dwarfism, Type Ii Kniest Chondrodystrophy Metatropic Dysplasia Type Ii Swiss Cheese Cartilage Dysplasia KD Ks Metatropic Dwarfism Type Ii Dysplasia, Kniest
Spondyloepimetaphyseal Dysplasia, Strudwick Type	Spondylometaphyseal Dysplasia Strudwick Syndrome Dappled Metaphysis Syndrome Semd, Strudwick Type Spondylometaepiphyseal Dysplasia Congenita, Strudwick Type Smed, Strudwick Type Smd Smed Strudwick Type SEMDSTWK Smed, Type I Semdc Smed Type 1 Spondyloepimetaphyseal Dysplasia Strudwick Type Sed Strudwick Spondyloepimetaphyseal Dysplasia Congenita, Strudwick Type Smed Type I Spondyloepiphyseal Dysplasia Congenita With Dappled Metaphyses Dysplasia, Spondyloepimetaphyseal, Strudwick Type Dysplasia, Spondylometaphyseal
Achondrogenesis, Type Ib	ACG1B Achondrogenesis Type Ib Achondrogenesis Type 1b Achondrogenesis Ib Achondrogenesis Fraccaro Type Achondrogenesis, Fraccaro Type Achondrogenesis, Parenti-Fraccaro Type Achondrogenesis 1b Acg-Ib Fraccaro Achondrogenesis
Retinal Detachment	Retinal Detachments Rhegmatogenous Retinal Detachment Ruptured Retina With Detachment Retinal Hole With Detachment
Fibrochondrogenesis	Fbcg1 Fbcg2 Fibrochondrogenesis-1 Fibrochondrogenesis-2 Fibrochondrogenesis 1 Fibrochondrogenesis 2
Otospondylomegaepiphyseal Dysplasia, Autosomal Dominant	Weissenbacher-Zweymuller Syndrome Wzs Pierre Robin Syndrome With Fetal Chondrodysplasia OSMEDA Weissenbacher-Zweymüller Syndrome Heterozygous Osmed Stickler Syndrome, Type 3 Osmed, Heterozygous Pierre Robin Syndrome With Fetal Chondrodysplasia Stickler Syndrome, Nonocular Type, Formerly Stickler Syndrome, Type Iii, Formerly Stl3, Formerly Piere-Robin Syndrome Pierre Robin Malformation Heterozygous Otospondylomegaepiphyseal Dysplasia Autosomal Dominant Otospondylomegaepiphyseal Dysplasia Ad Osmed Stickler Syndrome Type 3 Stickler Syndrome, Non-Ocular Type Stickler-Like Syndrome Stickler Syndrome 3 Stickler Syndrome Non-Ocular Type Stickler Syndrome Type Iii Stl3 Weissenbacher-Zweymueller Syndrome Stickler Syndrome, Type Iii Pierre Robin Syndrome Dysplasia, Otospondylomegaepiphyseal, Autosomal Dominant
Epiphyseal Dysplasia, Multiple, 1	EDM1 Multiple Epiphyseal Dysplasia 1 Multiple Epiphyseal Dysplasia Type 1 Med1 Multiple Epiphyseal Dysplasia Comp-Related Polyepiphyseal Dysplasia Type 1 Multiple Epiphyseal Dysplasia, Comp-Related Epiphyseal Dysplasia Multiple 1 Epiphyseal Dysplasia, Multiple 1 Dysplasia, Epiphyseal, Multiple, Type 1
Macroglossia	Congenital Macroglossia Enlarged Tongue Giant Tongue Acquired Macroglossia Nos Congenital Hypertrophy Of Tongue
Waardenburg Syndrome, Type 4b	Waardenburg Syndrome Type 4b WS4B Waardenburg Syndrome Type Ivb Waardenburg Syndrome With Hirschsprung Disease Type 4b Waardenburg Syndrome, Type 4b, With Hirschsprung Disease Waardenburg Syndrome, Type Ivb Waardenburg Syndrome 4b Hirschsprung Disease With Pigmentary Anomaly Shah-Waardenburg Syndrome Waardenburg-Shah Syndrome Waardenburg Syndrome, Type 4a
Spondyloepiphyseal Dysplasia Congenita	SEDC Sed Congenita Spondyloepiphyseal Dysplasia, Congenital Type Late Spondyloepiphyseal Dysplasia Sed, Congenital Type Congenital Spondyloepiphyseal Dysplasia Spranger-Wiedemann Disease Spondyloepiphyseal Dysplasia Congenital Type Dysplasia, Spondyloepiphyseal, Congenita Spondyloepiphyseal Dysplasia, Congenita Spondyloepiphyseal Dysplasia Tarda, X-Linked
Otospondylomegaepiphyseal Dysplasia, Autosomal Recessive	Osmed Otospondylomegaepiphyseal Dysplasia Chondrodystrophy With Sensorineural Deafness Nance-Insley Syndrome Nance-Sweeney Chondrodysplasia OSMEDB Insley-Astley Syndrome Osmed Syndrome Mega-Epiphyseal Dwarfism Weissenbacher-Zweymuller Syndrome, Formerly Wzs, Formerly Nance Sweeney Chondrodysplasia Oto-Spondylo-Mega-Epiphyseal Dysplasia Oto-Spondylo-Megaepiphyseal Dysplasia Megaepiphyseal Dwarfism
Hypochondrogenesis	Achondrogenesis Type Ii/Hypochondrogenesis
Fibrochondrogenesis 1	FBCG1 Fibrochondrogenesis, Type 1
Achondrogenesis	Achondrogenesis Syndrome
Spondyloperipheral Dysplasia	Spondyloperipheral Dysplasia With Short Ulna Spondyloperipheral Dysplasia-Short Ulna Syndrome SPD Dysplasia, Spondyloperipheral Spondyloperipheral Dysplasia Short Ulna
Treacher Collins Syndrome 1	Treacher Collins Syndrome Mandibulofacial Dysostosis Treacher Collins-Franceschetti Syndrome Tcof Tcs Mfd1 Franceschetti-Klein Syndrome TCS1 Franceschetti Syndrome Franceschetti-Zwahlen-Klein Syndrome Zygoauromandibular Dysplasia Treacher-Collins Syndrome Mandibulofacial Dysostosis Without Limb Anomalies Bilateral And Symmetric Oto-Mandibular Dysplasia
Osteochondrosis	Osteochondritis Apophysitis Epiphysitis Osteochondritis Juvenilis Epiphyseal Necrosis Juvenile Osteochondrosis Of Tibial Tubercle
Atelosteogenesis	Atelosteogenesis, Type 1
Spondyloepiphyseal Dysplasia With Congenital Joint Dislocations	Spondyloepiphyseal Dysplasia Chst3-Related Skeletal Dysplasia Humerospinal Dysostosis Spondyloepiphyseal Dysplasia, Omani Type Chondrodysplasia With Multiple Dislocations SEDCJD Hsd Cdmd Humero-Spinal Dysostosis Kozlowski Celermajer Tink Syndrome Chondrodysplasia With Congenital Joint Dislocations, Chst3 Type Larsen Syndrome, Recessive Type Humero-Spinal Dysostosis With Congenital Heart Disease Omani Type Sed Chst3 Deficiency Chst3-Related Dysplasia Recessive Larsen Syndrome Autosomal Recessive Larsen Syndrome Sed With Luxations, Chst3 Type Sed, Omani Type Sdcd, Chst3 Type Spondyloepiphyseal Dysplasia With Congenital Joint Dyslocations, Chst3 Type Sed Omani Type Spondyloepiphyseal Dysplasia Omani Type Larsen Syndrome, Autosomal Recessive Mucopolysaccharidosis Iv Spondyloepiphyseal Dysplasia, Congenita
Myopia	Near-Sightedness Short-Sightedness Nearsightedness Nearsighted Near Vision Close Sighted Myopic Short-Sighted Near Sighted
Strabismus	Strabismus, Susceptibility To Strabismus, Susceptibility To, 1 Strabismus 1
Diastrophic Dysplasia	Diastrophic Dwarfism DTD Dd Diastrophic Dysplasia, Broad Bone-Platyspondylic Variant Dysplasia, Diastrophic Diastrophic Dysplasia Variant
Achondrogenesis, Type Ii	Achondrogenesis Type Ii ACG2 Achondrogenesis, Langer-Saldino Type Achondrogenesis Type 2 Chondrogenesis Imperfecta Achondrogenesis, Type Ib, Formerly Achondrogenesis, Type Ii Or Hypochondrogenesis Achondrogenesis 2 Acg-Ii Achondrogenesis-Hypochondrogenesis Type Ii Achondrogenesis Langer-Saldino Type Achondrogenesis-Hypochondrogenesis, Type Ii Hypochondrogenesis
Donnai-Barrow Syndrome	Faciooculoacousticorenal Syndrome Dbs/Foar Syndrome Foar Syndrome Diaphragmatic Hernia-Exomphalos-Hypertelorism Syndrome Facio-Oculo-Acoustico-Renal Syndrome Diaphragmatic Hernia, Exomphalos, Absent Corpus Callosum, Hypertelorism, Myopia, Sensorineural Deafness, And Proteinuria Diaphragmatic Hernia-Hypertelorism-Myopia-Deafness Syndrome Holmes-Schepens Syndrome Syndrome Of Ocular And Facial Anomalies, Telecanthus And Deafness DBS Diaphragmatic Hernia Exomphalos Absent Corpus Callosum Hypertelorism Myopia Sensorineural Deafness And Proteinuria Diaphragmatic Hernia-Exomphalos-Corpus Callosum Agenesis Diaphragmatic Hernia-Hypertelorism-Myopia-Hearing Loss Syndrome Syndrome Of Ocular And Facial Anomalies, Telecanthus And Hearing Loss Donnai Barrow Syndrome
Retinal Perforation	Retinal Break Retinal Perforations Retinal Dialysis Retinal Tear Retinal Break Nos Ruptured Retina
Campomelic Dysplasia	Acampomelic Campomelic Dysplasia Camptomelic Dysplasia Campomelic Dysplasia With Autosomal Sex Reversal Cmpd CMD1 Cmpd1 Cmpd1/Sra1 Acampomelic Campomelic Dysplasia With Autosomal Sex Reversal Campomelic Dwarfism Campomelic Syndrome Dysplasia, Campomelic Chronic Myeloproliferative Disorder Familial Dilated Cardiomyopathy
Bone Development Disease
Cleft Palate, Isolated	Cleft Palate Isolated Cleft Palate CPI Cp Palatoschisis Cleft Palate Isolated Uranostaphyloschisis Congenital Fissure Of Palate Cleft Of Secondary Palate
Osteochondrodysplasia	Skeletal Dysplasia Chondrodystrophy Congenital Anomaly Of Cartilage Osteochondrodysplasias Cartilage Development Disorder Osteochondrodysplasia Syndrome Dysplasia, Skeletal Mucopolysaccharidosis Iv
Refractive Error	Refractive Errors
Cataract	Cataracts Cat - [Cataract] Cataract Form Lens Opacity Lens Opacities
Bethlem Myopathy 1	Bethlem Myopathy Myopathy, Benign Congenital, With Contractures Muscular Dystrophy, Benign Congenital BTHLM1 Muscular Dystrophy, Limb-Girdle, Autosomal Dominant 5 Lgmdd5 Benign Congenital Muscular Dystrophy Benign Autosomal Dominant Myopathy Myopathy, Bethlem Myopathy, Bethlem, Type 1
Ullrich Congenital Muscular Dystrophy 1	Ullrich Congenital Muscular Dystrophy Ullrich Disease Ucmd Ullrich Scleroatonic Muscular Dystrophy Scleroatonic Muscular Dystrophy UCMD1 Muscular Dystrophy, Limb-Girdle, Autosomal Recessive 22 Lgmdr22 Muscular Dystrophy, Scleroatonic Late Onset Scleroatonic Familial Myopathy Congenital Muscular Dystrophy, Ullrich Type
Orofacial Cleft	Cleft, Orofacial
Brittle Bone Disorder	Osteogenesis Imperfecta Brittle Bone Disease Fragilitas Ossium Osteopsathyrosis Lobstein Disease Oi Vrolik Disease Lobstein'S Disease Lobstein'S Syndrome Vrolik'S Disease Porak And Durante Disease Glass Bone Disease Osteogenesis Imperfecta, Dominant Perinatal Lethal Osteogenesis Imperfecta, Recessive Perinatal Lethal Brittle Bone Syndrome Oi - [Osteogenesis Imperfecta] Ossium Fragility Osteitis Fragilitans Bony Fragility Blue Sclera With Fragility Of Bone And Deafness White Blue Sclera - Fragility Of Bone - Deafness

Diseases	Alias
Waldenstroem'S Macroglobulinemia	Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma

Related Agents

Pre-clinical Phase

Pre-clinical Phase

Bioactive Molecules (3)

Cat. No.	Product Name	Effect	Purity	Rare Diseases
HY-RS03000	COL9A1 Human Pre-designed siRNA Set A	Pre-designed Set	/	Unkown
HY-RS20148	Col9a1 Mouse Pre-designed siRNA Set A	Pre-designed Set	/	Unkown
HY-RS26652	Col9a1 Rat Pre-designed siRNA Set A	Pre-designed Set	/	Unkown

Orthologs Information

Species	Symbol	Source	ID
Rattus norvegicus	COL9A1	RGD	RGD:1309425
Mus musculus	COL9A1	MGD	MGI:88465
Bos taurus	COL9A1	VGNC	VGNC:53787
Felis catus	COL9A1	VGNC	VGNC:61071
Canis familiaris	COL9A1	VGNC	VGNC:49782
Macaca mulatta	COL9A1	VGNC	VGNC:71306
Others	COL9A1	NCBI