MMP24

matrix metallopeptidase 24, the group of M10 matrix metallopeptidases

Basic information

Region (hg38): 20:35226690-35276998

Links

ENSG00000125966 ∙ NCBI:10893 ∙ OMIM:604871 ∙ HGNC:7172 ∙ Uniprot:Q9Y5R2 ∙ 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 MMP24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP24 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				1	1	2
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	2	1

Variants in MMP24

This is a list of pathogenic ClinVar variants found in the MMP24 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35226746-G-A		not specified	Uncertain significance (Apr 07, 2023)
20-35226757-G-A		not specified	Uncertain significance (Oct 10, 2023)
20-35226776-C-A		not specified	Uncertain significance (Apr 07, 2023)
20-35226779-C-A		not specified	Uncertain significance (Apr 07, 2023)
20-35226781-C-T		not specified	Likely benign (May 09, 2022)
20-35226791-C-T		not specified	Uncertain significance (Jul 25, 2023)
20-35226803-A-T		not specified	Uncertain significance (Apr 07, 2023)
20-35226830-T-C		not specified	Uncertain significance (Apr 07, 2023)
20-35226842-T-G		not specified	Uncertain significance (Nov 17, 2023)
20-35226878-C-T		not specified	Uncertain significance (Apr 12, 2024)
20-35226886-G-A		not specified	Uncertain significance (Apr 05, 2023)
20-35226886-G-C		not specified	Uncertain significance (Mar 23, 2022)
20-35226892-G-A		not specified	Uncertain significance (Aug 10, 2024)
20-35226956-A-C		not specified	Uncertain significance (Apr 07, 2023)
20-35226961-G-A		not specified	Uncertain significance (Apr 07, 2023)
20-35226962-C-T		not specified	Uncertain significance (Apr 07, 2023)
20-35226977-C-T		not specified	Uncertain significance (Apr 07, 2023)
20-35226979-G-A		not specified	Uncertain significance (Jul 20, 2021)
20-35246862-A-G		not specified	Uncertain significance (Dec 21, 2022)
20-35246882-C-T		not specified	Uncertain significance (Jun 03, 2022)
20-35246892-C-G		not specified	Uncertain significance (Oct 27, 2022)
20-35246910-C-T		not specified	Uncertain significance (Apr 23, 2024)
20-35246955-C-T		not specified	Uncertain significance (Oct 21, 2024)
20-35251922-G-A		not specified	Uncertain significance (Jul 12, 2023)
20-35251961-G-A		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP24	protein_coding	protein_coding	ENST00000246186	9	50345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.678	0.322	125544	0	9	125553	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.28	233	354	0.659	0.0000229	4142
Missense in Polyphen		89	172.55	0.51578		1821
Synonymous	0.796	133	145	0.916	0.00000991	1311
Loss of Function	3.77	5	25.6	0.195	0.00000123	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000935	0.0000913
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000652	0.0000616
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metalloprotease that mediates cleavage of N-cadherin (CDH2) and acts as a regulator of neuro-immune interactions and neural stem cell quiescence. Involved in cell-cell interactions between nociceptive neurites and mast cells, possibly by mediating cleavage of CDH2, thereby acting as a mediator of peripheral thermal nociception and inflammatory hyperalgesia. Key regulator of neural stem cells quiescence by mediating cleavage of CDH2, affecting CDH2-mediated anchorage of neural stem cells to ependymocytes in the adult subependymal zone, leading to modulate their quiescence. May play a role in axonal growth. Able to activate progelatinase A. May also be a proteoglycanase involved in degradation of proteoglycans, such as dermatan sulfate and chondroitin sulfate proteoglycans. Cleaves partially fibronectin, but not collagen type I, nor laminin (By similarity). {ECO:0000250}.
• Pathway: Matrix Metalloproteinases;Extracellular matrix organization;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.472
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.693
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmp24
• 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); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: proteolysis;glial cell differentiation;extracellular matrix organization;collagen catabolic process;positive regulation of catalytic activity;cell-cell adhesion mediated by cadherin;detection of temperature stimulus involved in sensory perception of pain;neuronal stem cell population maintenance;cell-cell adhesion via plasma-membrane adhesion molecules
• Cellular component: extracellular space;integral component of plasma membrane;extracellular matrix;trans-Golgi network membrane;extracellular exosome
• Molecular function: metalloendopeptidase activity;enzyme activator activity;zinc ion binding;cadherin binding