Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	1297
Gene name Gene Name - the full gene name approved by the HGNC.	Collagen type IX alpha 1 chain
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	COL9A1
Synonyms (NCBI Gene) Gene synonyms aliases	DJ149L1.1.2, EDM6, MED, STL4
Chromosome Chromosome number	6
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	6q13
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(16)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121912931	G>A	Pathogenic	Non coding transcript variant, upstream transcript variant, genic upstream transcript variant, stop gained, coding sequence variant
rs143848379	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, genic upstream transcript variant, missense variant
rs146700420	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, upstream transcript variant, genic upstream transcript variant, missense variant
rs149830493	A>T	Pathogenic, conflicting-interpretations-of-pathogenicity	Splice donor variant, upstream transcript variant, genic upstream transcript variant
rs189754995	G>A,T	Pathogenic	Coding sequence variant, non coding transcript variant, synonymous variant, stop gained, genic downstream transcript variant
rs201035486	G>A,C,T	Likely-pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, stop gained, missense variant, genic downstream transcript variant
rs202232444	C>G	Uncertain-significance, likely-pathogenic	Splice donor variant, genic upstream transcript variant, upstream transcript variant
rs374843706	C>A	Likely-pathogenic	Stop gained, coding sequence variant, genic downstream transcript variant, 5 prime UTR variant, non coding transcript variant
rs672601329	->A	Uncertain-significance, pathogenic	Genic upstream transcript variant, splice donor variant, upstream transcript variant
rs745532481	G>A	Pathogenic-likely-pathogenic	Non coding transcript variant, genic downstream transcript variant, stop gained, coding sequence variant
rs868122313	A>T	Likely-pathogenic	Genic downstream transcript variant, 5 prime UTR variant, stop gained, coding sequence variant, non coding transcript variant
rs1057519130	A>-	Likely-pathogenic	Genic upstream transcript variant, upstream transcript variant, coding sequence variant, frameshift variant
rs1064797325	->C	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1322800124	G>-,GG	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1554248926	A>-	Likely-pathogenic	Upstream transcript variant, coding sequence variant, genic upstream transcript variant, frameshift variant
rs1562305261	G>A	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, stop gained

Show/Hide all(172)

miRTarBase ID	miRNA	Experiments	Reference
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT495748	hsa-miR-1324	PAR-CLIP	22291592
MIRT495747	hsa-miR-3166	PAR-CLIP	22291592
MIRT495746	hsa-miR-4771	PAR-CLIP	22291592
MIRT495745	hsa-miR-1273h-3p	PAR-CLIP	22291592
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	27418678
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	27418678
MIRT610835	hsa-miR-8485	HITS-CLIP	27418678
MIRT610835	hsa-miR-8485	HITS-CLIP	27418678
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610835	hsa-miR-8485	HITS-CLIP	23824327
MIRT610834	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT610833	hsa-miR-6773-3p	HITS-CLIP	23824327
MIRT610832	hsa-miR-215-3p	HITS-CLIP	23824327
MIRT495748	hsa-miR-1324	PAR-CLIP	22291592
MIRT495747	hsa-miR-3166	PAR-CLIP	22291592
MIRT495746	hsa-miR-4771	PAR-CLIP	22291592
MIRT495745	hsa-miR-1273h-3p	PAR-CLIP	22291592
MIRT903225	hsa-miR-1206	CLIP-seq
MIRT903226	hsa-miR-1226	CLIP-seq
MIRT903227	hsa-miR-197	CLIP-seq
MIRT903228	hsa-miR-412	CLIP-seq
MIRT903229	hsa-miR-4502	CLIP-seq
MIRT903230	hsa-miR-4522	CLIP-seq
MIRT903231	hsa-miR-4733-3p	CLIP-seq
MIRT1967812	hsa-miR-34c-3p	CLIP-seq
MIRT1967813	hsa-miR-483-3p	CLIP-seq
MIRT1967814	hsa-miR-508-5p	CLIP-seq
MIRT1967815	hsa-miR-520a-5p	CLIP-seq
MIRT1967816	hsa-miR-525-5p	CLIP-seq

Show/Hide all(22)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	15047691, 32814053, 33961781
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005581	Component	Collagen trimer	IEA
GO:0005594	Component	Collagen type IX trimer	IBA
GO:0005594	Component	Collagen type IX trimer	IDA	8660302
GO:0005594	Component	Collagen type IX trimer	IPI	27897211
GO:0005594	Component	Collagen type IX trimer	TAS	9707347
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0009887	Process	Animal organ morphogenesis	IEA
GO:0009887	Process	Animal organ morphogenesis	TAS	3473493
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	IBA
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	IC	8660302
GO:0030020	Function	Extracellular matrix structural constituent conferring tensile strength	RCA	25037231
GO:0030246	Function	Carbohydrate binding	EXP	15047691
GO:0030246	Function	Carbohydrate binding	IMP	15047691
GO:0030246	Function	Carbohydrate binding	IPI	15047691, 17553797
GO:0031012	Component	Extracellular matrix	HDA	25037231
GO:0031012	Component	Extracellular matrix	IBA
GO:0042803	Function	Protein homodimerization activity	IPI	8660302
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
120210	2217	ENSG00000112280

Protein

UniProt ID

P20849

Protein name

Collagen alpha-1(IX) chain

Protein function

Structural component of hyaline cartilage and vitreous of the eye.

PDB

2UUR , 5CTD , 5CTI , 5CVA , 5CVB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01391	Collagen	266 → 326	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	303 → 358	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	357 → 409	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	415 → 474	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	454 → 531	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	643 → 716	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	697 → 760	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	785 → 849	Collagen triple helix repeat (20 copies)	Repeat

Sequence

MKTCWKIPVFFFVCSFLEPWASAAVKRRPRFPVNSNSNGGNELCPKIRIGQDDLPGFDLI
SQFQVDKAASRRAIQRVVGSATLQVAYKLGNNVDFRIPTRNLYPSGLPEEYSFLTTFRMT
GSTLKKNWNIWQIQDSSGKEQVGIKINGQTQSVVFSYKGLDGSLQTAAFSNLSSLFDSQW
HKIMIGVERSSATLFVDCNRIESLPIKPRGPIDIDGFAVLGKLADNPQVSVPFELQWMLI
HCDPLRPRRETCHELPARITPSQTTDERGPPGEQGPPGPPGPPGVPGIDGIDGDRGPKGP
PGPPGPAGEPGKPGAPGKPGTPGADGLTGPDGSPGSIGSKGQKGEPGVPGSRGFPGRGIP
GPPGPPGTAGLPGELGRVGPVGDPGRRGPPGPPGPPGPRGTIGFHDGDPLCPNACPPGRS
GYPGLPGMRGHKGAKGEIGEPGRQGHKGEEGDQGELGEVGAQGPPGAQGLRGITGIVGDK
GEKGARGLDGEPGPQGLPGAPGDQGQRGPPGEAGPKGDRGAEGARGIPGLPGPKGDTGLP
GVDGRDGIPGMPGTKGEPGKPGPPGDAGLQGLPGVPGIPGAKGVAGEKGSTGAPGKPGQM
GNSGKPGQQGPPGEVGPRGPQGLPGSRGELGPVGSPGLPGKLGSLGSPGLPGLPGPPGLP
GMKGDRGVVGEPGPKGEQGASGEEGEAGERGELGDIGLPGPKGSAGNPGEPGLRGPEGSR
GLPGVEGPRGPPGPRGVQGEQGATGLPGVQGPPGRAPTDQHIKQVCMRVIQEHFAEMAAS
LKRPDSGATGLPGRPGPPGPPGPPGENGFPGQMGIRGLPGIKGPPGALGLRGPKGDLGEK
GERGPPGRGPNGLPGAIGLPGDPGPASYGRNGRDGERGPPGVAGIPGVPGPPGPPGLPGF
CEPASCTMQAGQRAFNKGPDP

Sequence length

921

Interactions

View interactions

	KEGG		Reactome
	PI3K-Akt signaling pathway Focal adhesion ECM-receptor interaction Cytoskeleton in muscle cells Protein digestion and absorption Human papillomavirus infection		Collagen biosynthesis and modifying enzymes Signaling by PDGF Assembly of collagen fibrils and other multimeric structures Integrin cell surface interactions ECM proteoglycans NCAM1 interactions Collagen chain trimerization

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Connective Tissue Disease	Connective tissue disorder	rs189754995	N/A
Stickler Syndrome	Stickler syndrome, type 4	rs201035486, rs121912931, rs189754995	N/A

Show/Hide Unknown Diseases (6)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Epiphyseal dysplasia	epiphyseal dysplasia, multiple, 6	N/A	N/A	ClinVar
hearing impairment	Hearing impairment	N/A	N/A	ClinVar
Marfan Syndrome	marfan syndrome	N/A	N/A	ClinVar
Multiple Epiphyseal Dysplasia	Multiple Epiphyseal Dysplasia, Dominant	N/A	N/A	ClinVar
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
retinal dystrophy	Retinal dystrophy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (20)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
alpha Thalassemia	Associate	17301974
Carcinoma Squamous Cell	Associate	30657779
Cardiomyopathy Dilated	Associate	27936202
Cartilage Diseases	Associate	26973327, 27819742
Clubfoot	Associate	27819742
Collagenopathy type 2 alpha 1	Associate	33951325
Hearing Loss	Associate	31315069
Hypoxia	Stimulate	25510649
Insulin Resistance	Associate	27477082
Kashin Beck Disease	Associate	25774918
Musculoskeletal Abnormalities	Associate	31315069
Neoplasms	Associate	30657779
Nonsyndromic sensorineural hearing loss	Associate	31315069
Ossification of Posterior Longitudinal Ligament	Associate	30577800
Osteoarthritis	Associate	26973327, 32878268
Osteoarthritis Hip	Associate	15880806
Osteochondrodysplasias	Associate	11565064, 21922596, 30740902, 31315069, 39596690, 40392407
Patella Fracture	Associate	11565064
Peri Implantitis	Inhibit	25406169
Stickler syndrome type 1	Associate	16909383, 22522174, 31315069, 34405586

COL9A1 (collagen type IX alpha 1 chain)