MMP1

Chr 11

matrix metallopeptidase 1

ENSG00000196611 UniProt: P03956

Cleaves collagens of types I, II, and III at one site in the helical domain. Also cleaves collagens of types VII and X (PubMed:1645757, PubMed:2153297, PubMed:2557822). 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)

Research

ResearchGenerating clinical summary…

Active trials

450

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.52

LOEUF

Mechanism· predicted

Some data sources returned errors (2)

ncbi: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.52LOEUF

pLI 0.000

Z-score -0.41

OE 1.09 (0.80–1.52)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-1.12Z-score

OE missense 1.20 (1.09–1.31)

308 obs / 257.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.09 (0.80–1.52)

0≤0.351.4

Missense OE?1.20 (1.09–1.31)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 25 / 22.9Missense obs/exp: 308 / 257.6Syn Z: -0.07

Background carrier burden — how many people carry a rare variant somewhere in MMP1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 76

671 rare PASS variants

Rare truncating (LoF)

1 in 350

106 rare PASS variants

Rare synonymous (reference)

1 in 350

240 rare PASS variants

Rare missense and truncating variants are carried at similar rates in MMP1; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 100	1 in 320
South Asian	~43k	1 in 66	1 in 1,300
Remaining (unassigned)	~30k	1 in 56	1 in 250
European (Finnish)	~27k	1 in 150	1 in 1,700
Admixed American	~22k	1 in 55	1 in 310
African / African American	~21k	1 in 60	1 in 500
East Asian	~20k	1 in 82	1 in 580
Ashkenazi Jewish	~13k	1 in 210	1 in 1,400
Middle Eastern	~2,884	1 in 58	1 in 180

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 9 of 10 coding exons well covered in gnomAD exomes; exon 10 marginal. Genomes: all 10.? see exons ↓