MMP13 (matrix metallopeptidase 13)

Gene

• Entrez ID: 4322
• Gene name: Matrix metallopeptidase 13
• Gene symbol: MMP13
• Synonyms: CLG3, MANDP1, MDST, MMP-13
• Chromosome: 11
• Chromosome location: 11q22.2
• Summary: This gene encodes a member of the peptidase M10 family of matrix metalloproteinases (MMPs). Proteins in this family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and t

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs17860530	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs121909497	A>G	Pathogenic	Coding sequence variant, missense variant
rs121909498	A>G	Pathogenic	Coding sequence variant, missense variant
rs121909499	A>G	Pathogenic	Coding sequence variant, missense variant
rs121909500	G>T	Pathogenic	Coding sequence variant, missense variant
rs140059558	A>C,G	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs150203792	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs369083541	G>A	Pathogenic	Stop gained, coding sequence variant
rs374419716	A>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs797044754	->C	Pathogenic	Frameshift variant, coding sequence variant
rs1057518391	T>G	Likely-pathogenic	Splice acceptor variant
rs1565256477	A>G	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT000737	hsa-miR-199a-5p	Review	19574400
MIRT000734	hsa-miR-145-5p	Review	19574400
MIRT000025	hsa-miR-9-5p	Luciferase reporter assay	19008124
MIRT003427	hsa-miR-27b-3p	ELISA, Luciferase reporter assay, qRT-PCR, Western blot	20131257
MIRT003420	hsa-miR-100-5p	Microarray, qRT-PCR, Western blot	19396866
MIRT003961	hsa-miR-140-5p	Microarray	17875710
MIRT003961	hsa-miR-140-5p	qRT-PCR	19948051
MIRT006557	hsa-miR-27a-3p	qRT-PCR	19948051
MIRT006990	hsa-miR-125b-5p	Luciferase reporter assay	22782903
MIRT006990	hsa-miR-125b-5p	Luciferase reporter assay	22782903
MIRT021540	hsa-miR-143-3p	Western blot;Microarray	21427707
MIRT021796	hsa-miR-132-3p	Microarray	17612493
MIRT053120	hsa-miR-127-3p	Luciferase reporter assay	23762330
MIRT021540	hsa-miR-143-3p	Luciferase reporter assay	23732700
MIRT734854	hsa-miR-675-5p	Luciferase reporter assay, Western blotting, RNA-seq	33513878
MIRT736692	hsa-miR-579-3p	Luciferase reporter assay, Western blotting, qRT-PCR, Flow cytometry	33408506
MIRT756472	hsa-miR-182-5p	qRT-PCR	38796528
MIRT1153163	hsa-miR-204	CLIP-seq
MIRT1153164	hsa-miR-211	CLIP-seq
MIRT1153165	hsa-miR-3168	CLIP-seq
MIRT1153166	hsa-miR-340	CLIP-seq
MIRT1153167	hsa-miR-4755-5p	CLIP-seq
MIRT1153168	hsa-miR-4780	CLIP-seq
MIRT1153169	hsa-miR-513a-3p	CLIP-seq
MIRT1153170	hsa-miR-623	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
CITED2	Repression	12960175
ESR1	Unknown	19185056
ETS1	Activation	22270366
HDAC4	Repression	17656568;19423655
HDAC9	Activation	18054336
ING2	Activation	19437536
JUN	Activation	20338993
MAF	Activation	20067416
NFKB1	Activation	12734180;19022820
RELA	Activation	12734180;19022820
RUNX2	Activation	15564063
STAT1	Repression	17179173
YBX1	Repression	17822788

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004175	Function	Endopeptidase activity	IDA	18164633
GO:0004222	Function	Metalloendopeptidase activity	IBA	21873635
GO:0004222	Function	Metalloendopeptidase activity	IDA	8576151, 9065415
GO:0004222	Function	Metalloendopeptidase activity	TAS
GO:0005509	Function	Calcium ion binding	IDA	23913860
GO:0005518	Function	Collagen binding	IDA	9065415
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	TAS	8207000
GO:0006508	Process	Proteolysis	IEA
GO:0008270	Function	Zinc ion binding	IDA	23913860
GO:0022617	Process	Extracellular matrix disassembly	IMP	8576151, 9065415
GO:0022617	Process	Extracellular matrix disassembly	TAS
GO:0030198	Process	Extracellular matrix organization	IBA	21873635
GO:0030574	Process	Collagen catabolic process	IBA	21873635
GO:0030574	Process	Collagen catabolic process	IDA	8576151, 9065415
GO:0030574	Process	Collagen catabolic process	TAS
GO:0031012	Component	Extracellular matrix	IEA
GO:0060349	Process	Bone morphogenesis	IDA	16167086
GO:1904645	Process	Response to amyloid-beta	TAS	28912710

Other IDs

• MIM: 600108
• HGNC: 7159
• e!Ensembl: ENSG00000137745

Protein

• UniProt ID: P45452
• Protein name: Collagenase 3 (EC 3.4.24.-) (Matrix metalloproteinase-13) (MMP-13)
• Protein function: Plays a role in the degradation of extracellular matrix proteins including fibrillar collagen, fibronectin, TNC and ACAN. Cleaves triple helical collagens, including type I, type II and type III collagen, but has the highest activity with solubl
• PDB: 1EUB, 1FLS, 1FM1, 1PEX, 1XUC, 1XUD, 1XUR, 1YOU, 1ZTQ, 2D1N, 2E2D, 2OW9, 2OZR, 2PJT, 2YIG, 3ELM, 3I7G, 3I7I, 3KEC, 3KEJ, 3KEK, 3KRY, 3LJZ, 3O2X, 3TVC, 3WV1, 3WV2, 3WV3, 3ZXH, 456C, 4A7B, 4FU4, 4FVL, 4G0D, 4JP4, 4JPA, 4L19, 5B5O, 5B5P, 5BOT, 5BOY, 5BPA, 5UWK, 5UWL, 5UWM, 5UWN, 7JU8, 830C
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01471	PG_binding_1	32 → 91	Putative peptidoglycan binding domain	Domain
  PF00413	Peptidase_M10	112 → 267	Matrixin	Domain
  PF00045	Hemopexin	290 → 332	Hemopexin	Repeat
  PF00045	Hemopexin	334 → 377	Hemopexin	Repeat
  PF00045	Hemopexin	382 → 429	Hemopexin	Repeat
  PF00045	Hemopexin	431 → 471	Hemopexin	Repeat

• Sequence:

  MHPGVLAAFLFLSWTHCRALPLPSGGDEDDLSEEDLQFAERYLRSYYHPTNLAGILKENA
  ASSMTERLREMQSFFGLEVTGKLDDNTLDVMKKPRCGVPDVGEYNVFPRTLKWSKMNLTY
  RIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDG
  PSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALM
  FPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPNPKHPKTPDKCDPSLSLDAITSLRGET
  MIFKDRFFWRLHPQQVDAELFLTKSFWPELPNRIDAAYEHPSHDLIFIFRGRKFWALNGY
  DILEGYPKKISELGLPKEVKKISAAVHFEDTGKTLLFSGNQVWRYDDTNHIMDKDYPRLI
  EEDFPGIGDKVDAVYEKNGYIYFFNGPIQFEYSIWSNRIVRVMPANSILWC

• Sequence length: 471

Pathways

KEGG:

IL-17 signaling pathway
Relaxin signaling pathway
Parathyroid hormone synthesis, secretion and action

Reactome:

Collagen degradation
Degradation of the extracellular matrix
Activation of Matrix Metalloproteinases
Assembly of collagen fibrils and other multimeric structures
RUNX2 regulates genes involved in cell migration

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Arthritis	Degenerative polyarthritis	rs1594890601, rs1594882933, rs184370809, rs776489319, rs1594883470
Metaphyseal anadysplasia	Metaphyseal anadysplasia	rs121909498, rs121909499, rs140059558	19615667, 24781753
Metaphyseal chondrodysplasia	Metaphyseal chondrodysplasia, Metaphyseal chondrodysplasia Spahr type, Metaphyseal chondrodysplasia, Spahr type	rs121909500, rs121434597, rs121434598, rs121434600, rs121434602, rs199476103, rs727502774, rs1554651507, rs727502776, rs1554651446, rs727502778, rs1554651469, rs878853178, rs796065036, rs111033544, rs111033545, rs111033546, rs1562122372, rs111033543, rs111033547, rs111033549, rs111033550, rs111033551, rs111033552, rs111033548, rs111033553, rs111033554, rs111033556, rs2114276588, rs140059558, rs369083541, rs786204684, rs1554651506, rs753874439, rs1554651455, rs1085307765, rs1131691804, rs1383432106, rs1554651508, rs1340624774, rs751921616, rs551450545, rs752934195, rs549085067, rs1156413585, rs772443941, rs1554651395, rs1554651397, rs1554651396, rs1554651403, rs1554651424, rs1554651427, rs727502777, rs1230629953, rs1554651481, rs1554651491, rs1554651503, rs1554651532, rs1554651544, rs1554651365, rs1218494857, rs1587919129, rs1554651422, rs1554651428, rs1554651486, rs1554651489, rs1554651526, rs1554651405, rs1554651400, rs1587919165, rs1554651404, rs1554651411, rs1554651461, rs1554651471, rs1554651473, rs1554651505, rs781730798, rs1554651513, rs1554651153, rs759665242, rs1554651368, rs1554651382, rs1554651418, rs1554651413, rs1554651425, rs1554651451, rs1554651453, rs1554651462, rs1554651466, rs920074067, rs1554651499, rs1554651512, rs1554651524, rs1554651543, rs936059863, rs749667892, rs769180471, rs192060920, rs948931144, rs1554651373, rs1563907881, rs1563907883, rs1563907946, rs1563908212, rs1563908167, rs1582811858, rs1554651445	24648384, 24781753
Prostate cancer	Malignant neoplasm of prostate	rs121909139, rs121909140, rs121909141, rs121909142, rs121909143, rs606231169, rs606231170, rs137852584, rs137852578, rs137852580, rs137852581, rs137852582	15138554
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085
Spondyloepimetaphyseal dysplasia	Spondyloepimetaphyseal disorder, Spondyloepimetaphyseal Dysplasia, Missouri Type	rs121909497, rs121909499, rs879255602, rs878853267, rs779218846, rs878852980, rs878852981, rs1325869434, rs1565256477, rs1597675888, rs1597675890, rs1597676540, rs369033671	19615667, 24648384, 16167086

Unknown
Disease name	Disease term	dbSNP ID	References
Dwarfism	Dwarfism
Motor delay	Clumsiness - motor delay
Prostatic neoplasms	Prostatic Neoplasms		15138554
Rhizomelia	Rhizomelia
Rickets	Rickets