MMP25

matrix metallopeptidase 25, the group of M10 matrix metallopeptidases

Basic information

Region (hg38): 16:3046062-3060729

Previous symbols: [ "MMPL1", "MMP20" ]

Links

ENSG00000008516 ∙ NCBI:64386 ∙ OMIM:608482 ∙ HGNC:14246 ∙ Uniprot:Q9NPA2 ∙ 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 MMP25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMP25 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						0
missense			56	1		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	1	0

Variants in MMP25

This is a list of pathogenic ClinVar variants found in the MMP25 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3046936-C-T		not specified	Uncertain significance (Mar 04, 2024)
16-3046940-T-A		not specified	Uncertain significance (Feb 17, 2024)
16-3047002-G-A		not specified	Uncertain significance (Jul 16, 2021)
16-3047427-C-T		not specified	Uncertain significance (Feb 05, 2024)
16-3047452-A-C		not specified	Uncertain significance (Sep 16, 2021)
16-3047505-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-3047530-C-G		not specified	Uncertain significance (Sep 13, 2023)
16-3047538-G-T		not specified	Uncertain significance (Dec 07, 2022)
16-3050014-G-A		not specified	Uncertain significance (Jan 19, 2024)
16-3050086-C-T		not specified	Uncertain significance (Apr 12, 2024)
16-3050090-G-A		not specified	Uncertain significance (May 07, 2024)
16-3050095-C-T		not specified	Uncertain significance (Nov 13, 2023)
16-3050096-G-A		not specified	Uncertain significance (Jun 21, 2023)
16-3050108-G-A		not specified	Uncertain significance (Feb 26, 2024)
16-3050128-C-T		Mendelian syndromes with cleft lip/palate	Uncertain significance (-)
16-3050310-T-G		not specified	Uncertain significance (Oct 12, 2022)
16-3050412-G-A		not specified	Uncertain significance (Nov 07, 2022)
16-3050412-G-C		not specified	Uncertain significance (Jan 31, 2024)
16-3050414-G-A		not specified	Uncertain significance (Mar 03, 2022)
16-3050444-G-T		not specified	Uncertain significance (Dec 19, 2022)
16-3050463-C-A		not specified	Uncertain significance (May 20, 2024)
16-3050492-A-G		not specified	Uncertain significance (Feb 21, 2024)
16-3050501-G-T		not specified	Uncertain significance (Jan 20, 2023)
16-3057054-T-C		not specified	Uncertain significance (Nov 27, 2023)
16-3057110-C-T		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMP25	protein_coding	protein_coding	ENST00000336577	10	14046

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.73e-14	0.0711	125601	1	146	125748	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.879	387	341	1.13	0.0000199	3534
Missense in Polyphen		159	143.56	1.1075		1490
Synonymous	-1.97	183	152	1.20	0.00000929	1198
Loss of Function	0.595	22	25.2	0.872	0.00000137	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00128	0.00122
Ashkenazi Jewish	0.00	0.00
East Asian	0.000830	0.000761
Finnish	0.0000945	0.0000924
European (Non-Finnish)	0.000759	0.000730
Middle Eastern	0.000830	0.000761
South Asian	0.000461	0.000457
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May activate progelatinase A.
• Pathway: Matrix Metalloproteinases;Neutrophil degranulation;Extracellular matrix organization;Innate Immune System;Immune System;Activation of Matrix Metalloproteinases;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.310

Intolerance Scores

• loftool: 0.859
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.66

Haploinsufficiency Scores

• pHI: 0.429
• hipred: N
• hipred_score: 0.241
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.392

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mmp25

Zebrafish Information Network

• Gene name: mmp25b
• Affected structure: trigeminal sensory neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Biological process: proteolysis;inflammatory response;extracellular matrix organization;collagen catabolic process;neutrophil degranulation;hard palate development
• Cellular component: extracellular space;plasma membrane;membrane;integral component of membrane;extracellular matrix;anchored component of membrane;specific granule membrane
• Molecular function: metalloendopeptidase activity;zinc ion binding