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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	1299
Gene name	Collagen type IX alpha 3 chain
Gene symbol	COL9A3
Synonyms (NCBI Gene)	DJ885L7.4.1EDM3IDDMEDSTL6
Chromosome	20
Chromosome location	20q13.33
Summary	This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations i

Show/Hide all (13)

SNP ID	Visualize variation	Clinical significance	Consequence
rs61734651	C>T	Risk-factor, likely-benign, benign	Coding sequence variant, missense variant
rs146578812	C>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, 3 prime UTR variant, synonymous variant
rs150153886	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs606231367	G>A	Pathogenic	Splice acceptor variant
rs747896279	C>A,T	Pathogenic	Intron variant, coding sequence variant, stop gained, synonymous variant
rs766029215	G>A,T	Likely-pathogenic	Splice donor variant
rs1027769042	C>G,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, stop gained
rs1057518693	T>C	Pathogenic	Splice donor variant
rs1422176468	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1555821817	A>C	Likely-pathogenic	Intron variant
rs1555824129	C>G	Pathogenic	Coding sequence variant, missense variant
rs1600786629	A>T	Pathogenic	Splice acceptor variant
rs1600786748	G>A	Pathogenic	Intron variant

Show/Hide all (5)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018445	hsa-miR-335-5p	Microarray	18185580
MIRT903251	hsa-miR-129-5p	CLIP-seq
MIRT903252	hsa-miR-3137	CLIP-seq
MIRT903253	hsa-miR-3664-5p	CLIP-seq
MIRT903254	hsa-miR-4714-5p	CLIP-seq

Show/Hide all (14)

GO ID	Ontology	Definition	Evidence	Reference
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	8586434
GO:0005604	Component	Basement membrane	IBA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
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:0031012	Component	Extracellular matrix	HDA	25037231
GO:0042803	Function	Protein homodimerization activity	IPI	8660302

MIM	HGNC	e!Ensembl
120270	2219	ENSG00000092758

Q14050

Protein name

Collagen alpha-3(IX) chain

Protein function

Structural component of hyaline cartilage and vitreous of the eye.

PDB

5CTD , 5CTI , 5CVA , 5CVB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01391	Collagen	24 → 84	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	62 → 118	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	178 → 237	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	349 → 426	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	460 → 522	Collagen triple helix repeat (20 copies)	Repeat
PF01391	Collagen	549 → 610	Collagen triple helix repeat (20 copies)	Repeat

Sequence

MAGPRACAPLLLLLLLGELLAAAGAQRVGLPGPPGPPGPPGKPGQDGIDGEAGPPGLPGP
PGPKGAPGKPGKPGEAGLPGLPGVDGLTGRDGPPGPKGAPGERGSLGPPGPPGLGGKGLP
GPPGEAGVSGPPGGIGLRGPPGPSGLPGLPGPPGPPGPPGHPGVLPEGATDLQCPSICPP
GPPGPPGMPGFKGPTGYKGEQGEVGKDGEKGDPGPPGPAGLPGSVGLQGPRGLRGLPGPL
GPPGDRGPIGFRGPPGIPGAPGKAGDRGERGPEGFRGPKGDLGRPGPKGTPGVAGPSGEP
GMPGKDGQNGVPGLDGQKGEAGRNGAPGEKGPNGLPGLPGRAGSKGEKGERGRAGELGEA
GPSGEPGVPGDAGMPGERGEAGHRGSAGALGPQGPPGAPGVRGFQGQKGSMGDPGLPGPQ
GLRGDVGDRGPGGAAGPKGDQGIAGSDGLPGDKGELGPSGLVGPKGESGSRGELGPKGTQ
GPNGTSGVQGVPGPPGPLGLQGVPGVPGITGKPGVPGKEASEQRIRELCGGMISEQIAQL
AAHLRKPLAPGSIGRPGPAGPPGPPGPPGSIGHPGARGPPGYRGPTGELGDPGPRGNQGD
RGDKGAAGAGLDGPEGDQGPQGPQGVPGTSKDGQDGAPGEPGPPGDPGLPGAIGAQGTPG
ICDTSACQGAVLGGVGEKSGSRSS

Sequence length

684

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

276

Show/Hide Causal Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive Stickler syndrome	Likely pathogenic	rs2063547889	RCV001291129
COL9A3-related disorder	Pathogenic	rs1423359801, rs606231367	RCV003896898 RCV004730850
Connective tissue disorder	Likely pathogenic; Pathogenic	rs2147205530, rs2147208638	RCV002278707 RCV002278708
Epiphyseal dysplasia, multiple, 3	Pathogenic; Likely pathogenic	rs2147195552, rs1201247953, rs2516030998, rs1600786629, rs1600786748, rs606231367, rs1555821817, rs1991037713	RCV002238719 RCV002502051 RCV002283859 RCV000018676 RCV000018678 RCV004795925 RCV000578427 RCV001198019
Epiphyseal dysplasia, multiple, 3, with myopathy	Pathogenic	rs606231367	RCV000018679
Intervertebral disc disorder	Likely pathogenic; Pathogenic	rs1201247953	RCV002502051
Lattice retinal degeneration	Likely pathogenic	rs1384292566	RCV001283725
Retinal detachment	Likely pathogenic	rs1384292566	RCV001283725
Stickler syndrome	Pathogenic; Likely pathogenic	rs763259234, rs1201247953	RCV002238720 RCV002238721
Stickler syndrome, type 6	Pathogenic; Likely pathogenic	rs2147208658, rs1470627424, rs763259234, rs1201247953, rs989413835, rs2516029074, rs606231470, rs747896279	RCV002305621 RCV002279978 RCV002279980 RCV002279981 RCV002280060 RCV002280061 RCV002279937 RCV002279960

Show/Hide Unknown Diseases (27)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Adrenocortical carcinoma, hereditary	Benign	rs61734651	RCV005887550
Bilateral sensorineural hearing impairment	Uncertain significance	rs778892188	RCV000416549
Cervical cancer	Benign	rs116110757, rs3765462	RCV005919888 RCV005892530
Cholangiocarcinoma	Benign	rs61734651	RCV005887555
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs144292707	RCV005920584
Colon adenocarcinoma	Benign	rs61734651	RCV005887549
Colorectal cancer	Benign	rs2249903, rs61734651	RCV005892535 RCV005887552
Deafness	Uncertain significance	rs144292707	RCV005863616
Familial cancer of breast	Benign; Likely benign	rs6011413, rs2063642166	RCV005916908 RCV005926773
Gastric cancer	Likely benign; Benign	rs141943251, rs3765462	RCV005916412 RCV005892532
Glioma susceptibility 1	Uncertain significance	rs752954370	RCV005928733
Hearing impairment	Uncertain significance	rs746531996, rs759377762, rs758789140	RCV001375245 RCV001375157 RCV001375451
Intervertebral disc disease, susceptibility to	Benign	rs61734651	RCV000018677
Lung cancer	Likely benign	rs868516160	RCV005917493
Malignant lymphoma, large B-cell, diffuse	Benign	rs6011413	RCV005916910
Malignant tumor of esophagus	Benign	rs116110757	RCV005919887
Malignant tumor of urinary bladder	Uncertain significance	rs541379689	RCV005928676
Melanoma	Uncertain significance	rs1385900961	RCV005926503
Multiple Epiphyseal Dysplasia, Dominant	Uncertain significance; Likely benign	rs886056917, rs773103504, rs749822735, rs886056918	RCV000368477 RCV000394249 RCV000259505 RCV000300888
Ovarian serous cystadenocarcinoma	Likely benign; Benign	rs770204147, rs3765462	RCV005924238 RCV005892533
Sarcoma	Benign	rs116110757, rs3765462	RCV005919889 RCV005892531
Skeletal dysplasia	Conflicting classifications of pathogenicity	rs758064613	RCV005626600
Thymoma	Benign	rs6011413, rs61734651	RCV005916912 RCV005887554
Uterine carcinosarcoma	Benign; Conflicting classifications of pathogenicity	rs6011413, rs144292707, rs2249903, rs61734651, rs2294994	RCV005916911 RCV005920585 RCV005892536 RCV005887553 RCV005904144
Uterine corpus endometrial carcinoma	Uncertain significance; Benign	rs752954370, rs3765462, rs61734651	RCV005928734 RCV005892534 RCV005887556
Uveal melanoma	Benign	rs6011413, rs61734651	RCV005916909 RCV005887551
Vitreoretinopathy	Uncertain significance	rs1272918678	RCV005863732

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adrenoleukodystrophy	Associate	29476661
Alport Syndrome Mental Retardation Midface Hypoplasia and Elliptocytosis	Associate	33633367
Carcinoma Squamous Cell	Associate	33691689
Diabetes Mellitus Type 2	Associate	28427244
Encephalocele	Associate	21311409
Fibrocartilaginous embolism	Associate	16133074, 32943704
Fractures Bone	Associate	21311409
Fused Kidney	Associate	21311409
Hearing Loss	Associate	33078831
Hearing Loss Sensorineural	Associate	33570243, 33633367
Inflammation	Associate	29476661
Intervertebral Disc Degeneration	Associate	16133074
Intervertebral disc disease	Associate	14644861, 16133074, 16586133, 21311409, 38166944
Joint Diseases	Associate	33570243
Muscular Diseases	Associate	10655510, 20358595
Myopia	Associate	33570243
Nerve Degeneration	Associate	21311409
Neurodegenerative Diseases	Associate	16133074
Osteoarthritis	Associate	12096843
Osteoarthritis Knee	Associate	12096843
Osteochondrodysplasias	Associate	10090888, 10655510, 11565064, 20358595, 21922596, 25381065, 30740902, 33633367, 39596690
Retinal Degeneration	Associate	33570243, 33633367
Retinal Detachment	Associate	33633367
Sciatica	Associate	16133074
Spondylolisthesis	Associate	21311409
Stickler syndrome type 1	Associate	33570243, 33633367, 34405586, 34824372, 35241111

COL9A3 (collagen type IX alpha 3 chain)