COL9A3 (collagen type IX alpha 3 chain)

Gene

• Entrez ID: 1299
• Gene name: Collagen type IX alpha 3 chain
• Gene symbol: COL9A3
• Synonyms (NCBI Gene): DJ885L7.4.1, EDM3, IDD, MED, STL6
• Disease Acronyms (UniProt): EDM3, IDD, STL6
• 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

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005201	Function	Extracellular matrix structural constituent	IBA	21873635
GO:0005576	Component	Extracellular region	TAS
GO:0005594	Component	Collagen type IX trimer	IBA	21873635
GO:0005594	Component	Collagen type IX trimer	IDA	8660302
GO:0005604	Component	Basement membrane	IBA	21873635
GO:0005615	Component	Extracellular space	IBA	21873635
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0008584	Process	Male gonad development	IBA	21873635
GO:0008585	Process	Female gonad development	IBA	21873635
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:0030198	Process	Extracellular matrix organization	IBA	21873635
GO:0030198	Process	Extracellular matrix organization	TAS
GO:0031012	Component	Extracellular matrix	IBA	21873635
GO:0062023	Component	Collagen-containing extracellular matrix	HDA	25037231

Other IDs

• MIM: 120270
• HGNC: 2219
• e!Ensembl: ENSG00000092758

Protein

• UniProt ID: 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

Pathways

KEGG:

PI3K-Akt signaling pathway
Focal adhesion
ECM-receptor interaction
Cytoskeleton in muscle cells
Protein digestion and absorption
Human papillomavirus infection

Reactome:

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

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Arthritis	Degenerative polyarthritis	rs1594890601, rs1594882933, rs184370809, rs776489319, rs1594883470
Cataract	Cataract	rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322, rs121917775, rs121917735, rs121917736, rs137853199, rs137853200, rs121917867, rs121917869, rs121913555, rs104893736, rs121909595, rs121909596, rs121909597, rs28931605, rs121909598, rs104893618, rs1695062782, rs74315486, rs74315487, rs74315490, rs74315489, rs745938679, rs1566402656, rs74315439, rs74315441, rs121912973, rs121917823, rs1593332981, rs121917825, rs121917827, rs113994108, rs387906963, rs387906964, rs1240503246, rs387906965, rs387906966, rs750207077, rs387907336, rs387907337, rs387907342, rs140332366, rs397514703, rs398122937, rs398122378, rs398122392, rs398122944, rs137853924, rs398122947, rs397515623, rs397515624, rs397515625, rs397515626, rs398122948, rs587778872, rs398123066, rs587777601, rs370424081, rs786205221, rs786205222, rs864309684, rs864309688, rs864309701, rs864309689, rs864309690, rs864309681, rs864309686, rs864309696, rs864309693, rs864309687, rs864309691, rs864309692, rs864309695, rs864309678, rs864309685, rs864309700, rs864309698, rs864309683, rs864309682, rs864309679, rs111534978, rs864309680, rs864309702, rs864622780, rs756898971, rs869312732, rs775038545, rs878852983, rs1114167312, rs1114167313, rs1114167314, rs1114167315, rs1114167307, rs886041410, rs886041412, rs1057518738, rs1057517926, rs1057518878, rs1057519616, rs12799308, rs1064793935, rs1064797219, rs1085307126, rs1085307127, rs765628635, rs1114167427, rs1114167433, rs1554744860, rs1554743428, rs747093432, rs1411557416, rs1555179713, rs1481963503, rs1555549755, rs1456161420, rs1555547008, rs1555889308, rs1555888762, rs766522434, rs1264025914, rs1553585262, rs1567671947, rs1337897299, rs764945940, rs1307969607, rs949335475, rs1184095219, rs776129797, rs1569203234, rs1567668570, rs749141857, rs764098604, rs1184398243, rs1578956689, rs1568480054, rs1564745688, rs1564722302, rs1564723150, rs1571175950, rs1569602837, rs1576552712, rs1575369255, rs981126461, rs1570403798, rs200557771, rs1477743112, rs1651879427, rs1651881222, rs1651919374, rs2024441691, rs148284531, rs1246080692
Connective tissue disease	Connective Tissue Diseases	rs5742905, rs80338688, rs80356506, rs104894800, rs104894948, rs28931614, rs121913482, rs28933068, rs121913483, rs137854464, rs121912870, rs387906980, rs587777352, rs527236145, rs189754995, rs730880214, rs794728188, rs863223852, rs745672741, rs763514968, rs1064793914, rs1085307608, rs1131691804, rs1555399144, rs1554787779, rs1555167139, rs1939205327	15551337
Epiphyseal dysplasia	Epiphyseal dysplasia, EPIPHYSEAL DYSPLASIA, MULTIPLE, 3	rs137852652, rs28936668, rs1600786629, rs1600786748, rs606231367, rs1569763139, rs1569763108, rs1085307973, rs1555821817	15551337, 25381065, 24273071, 10090888, 10678658
Hearing loss	Sensorineural Hearing Loss (disorder)	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359, rs180177151, rs180177154, rs180177153, rs35689081, rs35887622, rs80338944, rs104894396, rs104894398, rs80338947, rs80338948, rs80338942, rs104894402, rs104894403, rs80338945, rs28931594, rs80338940, rs80338941, rs80356590, rs80338950, rs387906706, rs387906707, rs387906708, rs398122848, rs387907016, rs587776894, rs387907088, rs397515411, rs370965183, rs398122930, rs199897298, rs111033187, rs111033448, rs199606180, rs111033284, rs397516413, rs111033305, rs111033220, rs111033256, rs111033297, rs111033253, rs104894408, rs111033295, rs397516874, rs76434661, rs111033335, rs397517323, rs111033247, rs367928692, rs374793617, rs143939430, rs397515605, rs80338939, rs200656442, rs779748859, rs587781261, rs587781262, rs143343083, rs200147906, rs730880338, rs797044491, rs146281367, rs756484720, rs869025593, rs201306709, rs540895576, rs777777359, rs879255246, rs1554358720, rs142498437, rs377145777, rs1057517519, rs779077039, rs952741388, rs1060499797, rs764139009, rs1060499590, rs1064794012, rs1064797115, rs756790858, rs775633137, rs1554952443, rs1554952193, rs782063761, rs1199012623, rs756147087, rs1555648043, rs1555661490, rs1553196233, rs781546107, rs111033190, rs775428246, rs782539587, rs537227442, rs148695069, rs1554835827, rs953422571, rs1554834186, rs1554834161, rs1554835103, rs1554577339, rs1554577402, rs768471577, rs782279338, rs781951909, rs998045226, rs375759781, rs755804651, rs1557458426, rs767797828, rs538027448, rs1559366084, rs367688416, rs1558480402, rs1558490542, rs1559870857, rs1560690591, rs1561299289, rs1562817224, rs1562817529, rs1562822565, rs1562835391, rs1564113368, rs1564554255, rs773851192, rs1564555240, rs761261855, rs1564805114, rs1565522273, rs1565127413, rs781790246, rs1565430886, rs1565469959, rs746667217, rs1565819402, rs1565855932, rs150529554, rs1567939793, rs201866631, rs754472294, rs1559372512, rs1558464965, rs1558488902, rs775062249, rs1226171550, rs1561590396, rs765574676, rs762876554, rs757327146, rs1564949059, rs1565519673, rs368050948, rs1565541888, rs781989117, rs1565402473, rs750358148, rs1386887007, rs1209665716, rs1567641234, rs1237955948, rs1569042782, rs752672077, rs146689036, rs1560070780, rs149712664, rs1564556995, rs762226905, rs773573968, rs1568528171, rs1198256157, rs377267777, rs370564476, rs1577876794, rs747787770, rs759432278, rs1043716893, rs1581138934, rs2033773650, rs1421964916, rs771766431, rs780917129, rs1895773215, rs1895769400, rs761543680, rs1565920060
Multiple epiphyseal dysplasia	Multiple Epiphyseal Dysplasia, Multiple epiphyseal dysplasia due to collagen 9 anomaly	rs786200881, rs104893915, rs104893919, rs104893916, rs386833492, rs104893924, rs104893645, rs104893637, rs28939677, rs104893641, rs137852654, rs193922900, rs137852655, rs869320730, rs28936368, rs752248403, rs312262900, rs386833495, rs386833497, rs386833499, rs200963884, rs149551600, rs397515546, rs786204675, rs886039282, rs1057517523, rs1057517496, rs1057517462, rs1057517504, rs763198695, rs1057517483, rs1057517461, rs1057517524, rs1057517514, rs1057517526, rs1057517495, rs1057517532, rs1057517471, rs1057517502, rs1057517511, rs1057517482, rs1057517530, rs1057517474, rs762137330, rs1057517513, rs1014317450, rs1554095084, rs769859976, rs1554095145, rs1554095356, rs1554095374, rs1554095137, rs1554095156, rs745774620, rs1554095364, rs1481910744, rs1554095097, rs1554095125, rs1554095154, rs769657401, rs1554095381, rs1554095167, rs1554095266, rs1225601391, rs1554095296, rs1554095395, rs1235928535, rs1568554988, rs1561822760, rs1601054002, rs1601057167, rs1601054715, rs2055184939	15551337
Myopia	Myopia	rs387907109, rs146936371, rs587776903, rs786205127, rs398122836, rs199624584, rs587777625, rs786205216, rs758872875, rs764211125, rs1135402746, rs765658563, rs1555941129, rs1555941116, rs199923805, rs782555528, rs1554862601, rs1586620121, rs1387950081, rs2051026773, rs1422332023
Retinal detachment	Retinal Detachment	rs1555976049, rs1592230091
Stickler syndrome	Stickler syndrome (disorder), Stickler syndrome, type 1, Autosomal recessive Stickler syndrome	rs121912943, rs121912931, rs121912866, rs2136528572, rs121912869, rs121912870, rs121912872, rs121912873, rs121912876, rs794727377, rs2136508504, rs2136577259, rs121912882, rs1057524696, rs121912884, rs121912885, rs2136637244, rs121912893, rs1592232116, rs1592196064, rs121912896, rs121912897, rs121912898, rs80356554, rs606231376, rs398122828, rs189754995, rs672601354, rs672601355, rs748459670, rs886041713, rs886043356, rs886043410, rs886044244, rs1057517989, rs1057524114, rs72667036, rs1085307608, rs1131691822, rs1555165494, rs1553404310, rs1555166555, rs1553193910, rs1553223152, rs1555168965, rs1555164735, rs1555165204, rs1555166218, rs1555166295, rs1555166658, rs1025202963, rs1555168309, rs1246771678, rs866783525, rs201035486, rs1565679039, rs1557847904, rs1557877041, rs1557932876, rs1592233968, rs1592196744, rs1592217071, rs1592235241, rs1592202517, rs753342774, rs1592205758, rs1592206729, rs1269619781, rs1592196867, rs1592218346, rs1399676515, rs1939312423	18448257, 20686772, 31090205, 15802199, 24273071, 30450842

Associations from Text Mining
Disease Name	Relationship Type	References
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