COMP (cartilage oligomeric matrix protein)

Gene

• Entrez ID: 1311
• Gene name: Cartilage oligomeric matrix protein
• Gene symbol: COMP
• Synonyms: CTS2, EDM1, EPD1, MED, PSACH, THBS5, TSP-5, TSP5
• Chromosome: 19
• Chromosome location: 19p13.11
• Summary: The protein encoded by this gene is a noncollagenous extracellular matrix (ECM) protein. It consists of five identical glycoprotein subunits, each with EGF-like and calcium-binding (thrombospondin-like) domains. Oligomerization results from formation of a

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs28936368	G>A,T	Benign, pathogenic	Synonymous variant, coding sequence variant, missense variant
rs28936668	T>C	Pathogenic	Coding sequence variant, missense variant
rs28936669	T>C	Pathogenic	Coding sequence variant, missense variant
rs137852650	C>A	Pathogenic	Coding sequence variant, missense variant
rs137852651	C>T	Pathogenic	Coding sequence variant, missense variant
rs137852652	C>A	Pathogenic	Coding sequence variant, missense variant
rs137852653	A>G	Pathogenic	Coding sequence variant, missense variant
rs137852654	G>C,T	Likely-pathogenic	Coding sequence variant, missense variant
rs137852655	C>T	Pathogenic	Coding sequence variant, missense variant
rs137852656	A>G	Pathogenic	Coding sequence variant, missense variant
rs149551600	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs193922900	TCG>-,TCGTCG,TCGTCGTCG	Pathogenic, pathogenic-likely-pathogenic	Inframe insertion, coding sequence variant, inframe deletion
rs312262899	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs312262900	G>A,C,T	Pathogenic	Missense variant, coding sequence variant
rs312262901	T>C	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs312262903	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs312262904	C>T	Pathogenic	Missense variant, coding sequence variant
rs374063820	A>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs397515510	TGT>-	Pathogenic	Inframe deletion, coding sequence variant
rs397515511	G>T	Pathogenic	Coding sequence variant, missense variant
rs397515512	C>T	Pathogenic	Coding sequence variant, missense variant
rs397515513	G>C	Pathogenic	Coding sequence variant, missense variant
rs755374221	C>A,T	Likely-pathogenic	Splice donor variant
rs869320730	->G	Pathogenic	Frameshift variant, coding sequence variant
rs878853098	GCATCTCCCACAA>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs886041607	C>A	Pathogenic	Missense variant, coding sequence variant
rs886042932	C>G,T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs1057521130	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1064794293	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1064794294	TCGTCC>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs1131691682	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1131691835	C>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1359984033	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs1555791425	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1555791490	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1555791556	C>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1568554484	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1568554988	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1601053887	CCT>-	Pathogenic	Inframe deletion, coding sequence variant
rs1601053997	C>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1601054002	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant
rs1601054715	C>A	Pathogenic	Coding sequence variant, missense variant
rs1601055900	GCGCTGGTCTGGGTT>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1601055923	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1601057057	T>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1601057167	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1601057491	T>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1601057570	A>G	Likely-pathogenic	Coding sequence variant, missense variant

Transcription factors

Transcription factor	Regulation	Reference
LRF	Unknown	15337766
SP1	Unknown	11223338

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	TAS	7670472
GO:0002020	Function	Protease binding	IPI	18485748
GO:0002063	Process	Chondrocyte development	IEA
GO:0003417	Process	Growth plate cartilage development	IEA
GO:0005178	Function	Integrin binding	IEA
GO:0005201	Function	Extracellular matrix structural constituent	RCA	20551380
GO:0005509	Function	Calcium ion binding	IDA	10852928, 11084047
GO:0005515	Function	Protein binding	IPI	12225811, 15075323, 16051604, 16611630, 17588949, 18485748, 25416956, 31515488, 32296183
GO:0005518	Function	Collagen binding	IDA	11084047
GO:0005576	Component	Extracellular region	HDA	27068509
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	HDA	20551380
GO:0006915	Process	Apoptotic process	IEA
GO:0006986	Process	Response to unfolded protein	IEA
GO:0008201	Function	Heparin binding	IDA	17588949
GO:0009306	Process	Protein secretion	IEA
GO:0009887	Process	Animal organ morphogenesis	TAS	7713493
GO:0010259	Process	Multicellular organism aging	IEA
GO:0010260	Process	Animal organ senescence	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0014829	Process	Vascular associated smooth muscle contraction	IEA
GO:0016485	Process	Protein processing	IEA
GO:0030198	Process	Extracellular matrix organization	TAS
GO:0030199	Process	Collagen fibril organization	IEA
GO:0030282	Process	Bone mineralization	IEA
GO:0030500	Process	Regulation of bone mineralization	IEA
GO:0030509	Process	BMP signaling pathway	IEA
GO:0031012	Component	Extracellular matrix	TAS	7713493
GO:0032991	Component	Protein-containing complex	IEA
GO:0035264	Process	Multicellular organism growth	IEA
GO:0035988	Process	Chondrocyte proliferation	IEA
GO:0035989	Process	Tendon development	IEA
GO:0036122	Function	BMP binding	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IDA	17993464
GO:0043394	Function	Proteoglycan binding	IDA	29030641
GO:0043395	Function	Heparan sulfate proteoglycan binding	IDA	17588949
GO:0043588	Process	Skin development	IEA
GO:0048747	Process	Muscle fiber development	IEA
GO:0048844	Process	Artery morphogenesis	IEA
GO:0050881	Process	Musculoskeletal movement	IEA
GO:0050905	Process	Neuromuscular process	IEA
GO:0060173	Process	Limb development	IDA	16542502
GO:0062023	Component	Collagen-containing extracellular matrix	HDA	20551380
GO:0062023	Component	Collagen-containing extracellular matrix	IBA	21873635
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0070527	Process	Platelet aggregation	IEA
GO:0097084	Process	Vascular associated smooth muscle cell development	IEA
GO:1900047	Process	Negative regulation of hemostasis	IEA
GO:1902732	Process	Positive regulation of chondrocyte proliferation	IEA

Other IDs

• MIM: 600310
• HGNC: 2227
• e!Ensembl: ENSG00000105664

Protein

• UniProt ID: P49747
• Protein name: Cartilage oligomeric matrix protein (COMP) (Thrombospondin-5) (TSP5)
• Protein function: Plays a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as the collagens and fibronectin. Can mediate the interaction of chondrocytes with the cartilage extracellular matrix through
• PDB: 3FBY
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF11598	COMP	29 → 73	Cartilage oligomeric matrix protein	Family
  PF07645	EGF_CA	127 → 178	Calcium-binding EGF domain	Domain
  PF07645	EGF_CA	180 → 221	Calcium-binding EGF domain	Domain
  PF02412	TSP_3	301 → 336	Thrombospondin type 3 repeat	Repeat
  PF02412	TSP_3	360 → 395	Thrombospondin type 3 repeat	Repeat
  PF02412	TSP_3	395 → 418	Thrombospondin type 3 repeat	Repeat
  PF02412	TSP_3	419 → 456	Thrombospondin type 3 repeat	Repeat
  PF02412	TSP_3	457 → 492	Thrombospondin type 3 repeat	Repeat
  PF02412	TSP_3	493 → 528	Thrombospondin type 3 repeat	Repeat
  PF05735	TSP_C	546 → 743	Thrombospondin C-terminal region	Family

• Sequence:

  MVPDTACVLLLTLAALGASGQGQSPLGSDLGPQMLRELQETNAALQDVRELLRQQVREIT
  FLKNTVMECDACGMQQSVRTGLPSVRPLLHCAPGFCFPGVACIQTESGARCGPCPAGFTG
  NGSHCTDVNECNAHPCFPRVRCINTSPGFRCEACPPGYSGPTHQGVGLAFAKANKQVCTD
  INECETGQHNCVPNSVCINTRGSFQCGPCQPGFVGDQASGCQRRAQRFCPDGSPSECHEH
  ADCVLERDGSRSCVCAVGWAGNGILCGRDTDLDGFPDEKLRCPERQCRKDNCVTVPNSGQ
  EDVDRDGIGDACDPDADGDGVPNEKDNCPLVRNPDQRNTDEDKWGDACDNCRSQKNDDQK
  DTDQDGRGDACDDDIDGDRIRNQADNCPRVPNSDQKDSDGDGIGDACDNCPQKSNPDQAD
  VDHDFVGDACDSDQDQDGDGHQDSRDNCPTVPNSAQEDSDHDGQGDACDDDDDNDGVPDS
  RDNCRLVPNPGQEDADRDGVGDVCQDDFDADKVVDKIDVCPENAEVTLTDFRAFQTVVLD
  PEGDAQIDPNWVVLNQGREIVQTMNSDPGLAVGYTAFNGVDFEGTFHVNTVTDDDYAGFI
  FGYQDSSSFYVVMWKQMEQTYWQANPFRAVAEPGIQLKAVKSSTGPGEQLRNALWHTGDT
  ESQVRLLWKDPRNVGWKDKKSYRWFLQHRPQVGYIRVRFYEGPELVADSNVVLDTTMRGG
  RLGVFCFSQENIIWANLRYRCNDTIPEDYETHQLRQA

• Sequence length: 757

Pathways

KEGG:

Phagosome
PI3K-Akt signaling pathway
Focal adhesion
ECM-receptor interaction
Cytoskeleton in muscle cells
Malaria
Human papillomavirus infection

Reactome:

Integrin cell surface interactions
ECM proteoglycans

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Arthritis	Degenerative polyarthritis	rs1594890601, rs1594882933, rs184370809, rs776489319, rs1594883470	7670472
Brachydactyly	Brachydactyly	rs121908949, rs28937580, rs121909082, rs104894122, rs863223289, rs863223290, rs104894121, rs1587657302, rs863223292, rs74315386, rs74315387, rs28936397, rs753691079, rs121909348, rs121917852, rs121917853, rs121917854, rs121917855, rs121917859, rs121917861, rs267606873, rs267606872, rs267606985, rs267606986, rs267606987, rs267606988, rs28933082, rs397514519, rs869025613, rs869025614, rs886039878, rs1553540620, rs1057518333, rs1948841937, rs1948868228, rs1948842030, rs1948842142
Epiphyseal dysplasia	Epiphyseal dysplasia, Epiphyseal dysplasia, multiple, 1	rs137852652, rs28936668, rs1600786629, rs1600786748, rs606231367, rs1569763139, rs1569763108, rs1085307973, rs1555821817	7670472, 9463320, 17133256, 11084047, 21922596, 11565064, 9021009, 15523498, 9887340, 9184241, 9452026, 9921895, 27330822
Multiple epiphyseal dysplasia	Multiple epiphyseal dysplasia type 1	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
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085

Unknown
Disease name	Disease term	dbSNP ID	References
Avascular necrosis of the capital femoral epiphysis	Avascular necrosis of the capital femoral epiphysis
Congenital genu recurvatum	Congenital genu recurvatum
Dwarfism	Dwarfism
Hamartomatous polyposis	Hamartomatous polyposis
Intestinal polyposis	Intestinal Polyposis
Legg-calve-perthes disease	Legg-Calve-Perthes Disease
Micromelia	Micromelia
Osteoarthritis of hip	Osteoarthritis of hip		28319091
Osteoarthrosis deformans	Osteoarthrosis Deformans		7670472
Pseudoachondroplasia	Pseudoachondroplasia, PSEUDOACHONDROPLASIA, SEVERE		11084047, 7670472, 9463320, 9184241, 21922596, 9887340, 7670471, 9921895, 11746044, 11746045, 10852928, 9452063, 9452026, 9021009
Sensory neuropathy	Sensory neuropathy