MMP25

Chr 16

matrix metallopeptidase 25

Also known as: MMP-25, MMP20, MMP20A, MMPL1, MT-MMP 6, MT-MMP6, MT6-MMP, MT6MMP

NCBI Gene: 64386ENSG00000008516UniProt: Q9H239OMIM: 608482

MMP25 encodes a membrane-type matrix metalloproteinase that degrades extracellular matrix components and inactivates alpha-1 proteinase inhibitor during inflammatory responses, facilitating neutrophil migration to inflammatory sites. The gene shows very low constraint against loss-of-function variants (pLI near zero), and no established Mendelian disease associations have been reported to date. Current evidence suggests this gene may not be critical for normal human development or associated with pediatric neurological disorders.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.25
Clinical Summary— MMP25
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
35 unique Pathogenic / Likely Pathogenic· 144 VUS of 191 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.25LOEUF
pLI 0.000
Z-score 0.60
OE 0.87 (0.62–1.25)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.88Z-score
OE missense 1.13 (1.04–1.23)
387 obs / 341.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.87 (0.62–1.25)
0≤0.351.4
Missense OE1.13 (1.04–1.23)
0≤0.61.4
Synonymous OE1.20
0≤1.21.6
LoF obs/exp: 22 / 25.2Missense obs/exp: 387 / 341.3Syn Z: -1.97
DN
0.6743th %ile
GOF
0.6735th %ile
LOF
0.3552th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

191 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic35
VUS144
Likely Benign3
35
Pathogenic
144
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
35
0
35
Likely Pathogenic
0
0
0
0
0
VUS
1
133
10
0
144
Likely Benign
0
2
1
0
3
Benign
0
0
0
0
0
Total1135460182

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

MMP25 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients