MMP1

matrix metallopeptidase 1, the group of Receptor ligands|M10 matrix metallopeptidases

Basic information

Region (hg38): 11:102789400-102798160

Previous symbols: [ "CLG" ]

Links

ENSG00000196611 ∙ NCBI:4312 ∙ OMIM:120353 ∙ HGNC:7155 ∙ Uniprot:P03956 ∙ 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 MMP1 gene.

• not provided (38 variants)
• Inborn genetic diseases (23 variants)
• not specified (6 variants)
• Preterm premature rupture of membranes (1 variants)
• Recessive dystrophic epidermolysis bullosa;COPD, severe early onset (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP1 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				2	3	5
missense			21	6	1	28
nonsense			1			1
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					27	27
Total	0	0	22	8	32

Variants in MMP1

This is a list of pathogenic ClinVar variants found in the MMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-102790143-G-A			Benign (Jun 19, 2021)
11-102790228-A-G			Benign (Nov 12, 2018)
11-102790349-G-A			Benign (Jun 19, 2021)
11-102790368-T-C			Benign (Jun 19, 2021)
11-102790421-C-A		not specified	Uncertain significance (Dec 16, 2021)
11-102790433-C-T		not specified	Uncertain significance (May 04, 2022)
11-102790545-T-G			Benign (Nov 12, 2018)
11-102790704-A-G			Benign (Dec 31, 2019)
11-102790787-A-T			Likely benign (Dec 31, 2019)
11-102790864-A-G			Benign (Jun 19, 2021)
11-102790934-G-A			Benign (Nov 12, 2018)
11-102791026-G-A			Benign (Nov 12, 2018)
11-102791082-G-C			Benign (Nov 12, 2018)
11-102791357-A-C		not specified	Uncertain significance (Aug 17, 2022)
11-102791397-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-102791400-T-C		not specified	Uncertain significance (Jun 01, 2022)
11-102791409-C-T		MMP1-related disorder	Benign/Likely benign (Mar 18, 2020)
11-102791492-T-G		not specified	Uncertain significance (Feb 22, 2023)
11-102791499-C-T		MMP1-related disorder	Likely benign (Jul 11, 2022)
11-102791735-T-C			Benign (Jun 20, 2021)
11-102792632-C-T		not specified	Uncertain significance (Mar 24, 2023)
11-102792641-C-T		not specified	Uncertain significance (Aug 04, 2023)
11-102792642-G-A			Likely benign (Dec 31, 2019)
11-102792649-GC-G		Interstitial lung disease 2	Uncertain significance (May 06, 2018)
11-102792725-T-C		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP1	protein_coding	protein_coding	ENST00000315274	10	8241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.72e-18	0.00214	122374	24	3347	125745	0.0135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.12	308	258	1.20	0.0000134	3131
Missense in Polyphen		112	95.573	1.1719		1190
Synonymous	-0.0725	92	91.1	1.01	0.00000487	860
Loss of Function	-0.413	25	22.9	1.09	0.00000107	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0131	0.0131
Ashkenazi Jewish	0.00427	0.00428
East Asian	0.00158	0.00158
Finnish	0.0126	0.0125
European (Non-Finnish)	0.0201	0.0201
Middle Eastern	0.00158	0.00158
South Asian	0.00964	0.00945
Other	0.0141	0.0139

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves collagens of types I, II, and III at one site in the helical domain. Also cleaves collagens of types VII and X (PubMed:2557822, PubMed:2153297, PubMed:1645757). In case of HIV infection, interacts and cleaves the secreted viral Tat protein, leading to a decrease in neuronal Tat's mediated neurotoxicity (PubMed:16807369). {ECO:0000269|PubMed:1645757, ECO:0000269|PubMed:16807369, ECO:0000269|PubMed:2153297, ECO:0000269|PubMed:2557822}.
• Pathway: Relaxin signaling pathway - Homo sapiens (human);Bladder cancer - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Matrix Metalloproteinases;Oncostatin M Signaling Pathway;Quercetin and Nf-kB- AP-1 Induced Cell Apoptosis;Bladder Cancer;Photodynamic therapy-induced NF-kB survival signaling;Hepatitis C and Hepatocellular Carcinoma;TGF-beta Signaling Pathway;PPAR signaling pathway;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;Metabolism of proteins;Collagen formation;Extracellular matrix organization;Activation of Matrix Metalloproteinases;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Glucocorticoid receptor regulatory network;Cell surface interactions at the vascular wall;Hemostasis;Degradation of the extracellular matrix;EGFR Transactivation by Gastrin;Posttranslational regulation of adherens junction stability and dissassembly;Basigin interactions;Gastrin-CREB signalling pathway via PKC and MAPK;G alpha (q) signalling events;GPCR downstream signalling;AP-1 transcription factor network;Syndecan-1-mediated signaling events;p75(NTR)-mediated signaling;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Validated transcriptional targets of AP1 family members Fra1 and Fra2;Endothelins (Consensus)

Recessive Scores

• pRec: 0.810

Intolerance Scores

• loftool: 0.907
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.27

Haploinsufficiency Scores

• pHI: 0.487
• hipred: N
• hipred_score: 0.209
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.851

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmp1b

Gene ontology

• Biological process: proteolysis;viral process;cytokine-mediated signaling pathway;extracellular matrix disassembly;extracellular matrix organization;collagen catabolic process;positive regulation of protein oligomerization;cellular protein metabolic process;leukocyte migration
• Cellular component: extracellular region;extracellular space;extracellular matrix
• Molecular function: endopeptidase activity;metalloendopeptidase activity;serine-type endopeptidase activity;zinc ion binding