MMP3

matrix metallopeptidase 3, the group of M10 matrix metallopeptidases

Basic information

Region (hg38): 11:102835800-102843609

Previous symbols: [ "STMY1", "STMY" ]

Links

ENSG00000149968 ∙ NCBI:4314 ∙ OMIM:185250 ∙ HGNC:7173 ∙ Uniprot:P08254 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MMP3 gene.

• not provided (32 variants)
• Inborn genetic diseases (20 variants)
• not specified (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	8	12
missense			20	3	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region					1	1
non coding					14	14
Total	0	0	20	7	24

Variants in MMP3

This is a list of pathogenic ClinVar variants found in the MMP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-102836175-G-C		not specified	Uncertain significance (Apr 13, 2022)
11-102836574-G-A			Benign (Nov 12, 2018)
11-102837183-A-G			Benign (Nov 12, 2018)
11-102837312-A-G		not specified	Uncertain significance (Jun 24, 2022)
11-102837326-T-C			Likely benign (May 17, 2018)
11-102837331-C-A		not specified	Uncertain significance (Jan 07, 2022)
11-102837357-T-C		not specified	Uncertain significance (Feb 26, 2024)
11-102838611-G-A		not specified	Uncertain significance (Oct 03, 2022)
11-102838615-C-T		not specified	Uncertain significance (Jul 27, 2022)
11-102838649-G-A			Benign (Jul 15, 2018)
11-102838654-T-A		not specified	Uncertain significance (Jul 19, 2022)
11-102838694-A-G		not specified	Benign (Nov 12, 2018)
11-102838730-CAG-C			Benign (Nov 12, 2018)
11-102838791-T-A			Benign (Nov 12, 2018)
11-102839190-G-T		not specified	Uncertain significance (May 24, 2023)
11-102839209-G-A		not specified	Uncertain significance (May 09, 2023)
11-102839216-C-A		not specified	Uncertain significance (Apr 07, 2022)
11-102839352-G-A			Benign (Jun 21, 2021)
11-102839976-T-A			Benign (Nov 12, 2018)
11-102840185-C-A			Benign (Jul 23, 2018)
11-102840213-G-A		not specified	Uncertain significance (Oct 20, 2021)
11-102840228-G-T		not specified	Uncertain significance (Feb 13, 2024)
11-102840234-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-102840251-T-C		MMP3-related disorder	Benign/Likely benign (Dec 31, 2019)
11-102840431-T-C		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP3	protein_coding	protein_coding	ENST00000299855	10	8003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.74e-15	0.0146	125591	0	155	125746	0.000617

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.644	285	256	1.11	0.0000128	3136
Missense in Polyphen		94	80.177	1.1724		1004
Synonymous	-1.38	114	96.8	1.18	0.00000515	920
Loss of Function	0.0341	22	22.2	0.992	0.00000112	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00221	0.00220
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000926	0.000925
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000364	0.000360
Middle Eastern	0.000926	0.000925
South Asian	0.00115	0.00114
Other	0.000983	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can degrade fibronectin, laminin, gelatins of type I, III, IV, and V; collagens III, IV, X, and IX, and cartilage proteoglycans. Activates procollagenase.
• Disease: DISEASE: Coronary heart disease 6 (CHDS6) [MIM:614466]: A multifactorial disease characterized by an imbalance between myocardial functional requirements and the capacity of the coronary vessels to supply sufficient blood flow. Decreased capacity of the coronary vessels is often associated with thickening and loss of elasticity of the coronary arteries. {ECO:0000269|PubMed:12477941, ECO:0000269|PubMed:8662692}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. A polymorphism in the MMP3 promoter region is associated with the risk of coronary heart disease and myocardial infarction, due to lower MMP3 proteolytic activity and higher extracellular matrix deposition in atherosclerotic lesions.
• Pathway: TNF signaling pathway - Homo sapiens (human);Prostate cancer - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Matrix Metalloproteinases;Oncostatin M Signaling Pathway;Photodynamic therapy-induced NF-kB survival signaling;Protein alkylation leading to liver fibrosis;Interleukin-4 and 13 signaling;Signaling by GPCR;Assembly of collagen fibrils and other multimeric structures;Signal Transduction;Collagen degradation;Collagen formation;Extracellular matrix organization;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix;EGFR Transactivation by Gastrin;Posttranslational regulation of adherens junction stability and dissassembly;Gastrin-CREB signalling pathway via PKC and MAPK;G alpha (q) signalling events;GPCR downstream signalling;p75(NTR)-mediated signaling;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.866

Intolerance Scores

• loftool: 0.898
• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.91

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.182
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.589

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mmp3
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: proteolysis;negative regulation of hydrogen peroxide metabolic process;cytokine-mediated signaling pathway;extracellular matrix disassembly;extracellular matrix organization;collagen catabolic process;positive regulation of protein oligomerization;cellular response to nitric oxide;regulation of neuroinflammatory response;positive regulation of oxidative stress-induced cell death
• Cellular component: extracellular region;extracellular space;extracellular matrix
• Molecular function: endopeptidase activity;metalloendopeptidase activity;serine-type endopeptidase activity;protein binding;metallopeptidase activity;zinc ion binding